tag:blogger.com,1999:blog-116432542024-03-18T17:54:49.139+00:00MetallomeMetals: facts, factoids and some not quite related stuff tooKirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.comBlogger186125tag:blogger.com,1999:blog-11643254.post-20376351073195685842024-03-10T20:00:00.015+00:002024-03-16T10:28:09.826+00:00α, β, ξ<p> Here’s a molecule everybody must have heard about: <a href="http://en.wikipedia.org/wiki/Testosterone" target="_blank" title="Testosterone in Wikipedia">testosterone</a> <b>(a)</b>. </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17347" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="testosterone (CHEBI:17347)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEin161Sg1NXZVFNpYsyAsQcM1oMq9bLQBjIgbwkn853UZAyZFG84x-m2CwEQglGCE1-8DK4rQAKAKT1IvVIJe-ibxOEBWFt8QeM4bHKaVXf4v40J74GyjJaMlIi0GO99bjXtotmkxJE13AajgXITtMzU6Tl324R0Omtay-WHUZrEpQzn24bsdi7Rw/s1600/testosterone.png" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th>
</tr></tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="1" type="a">
<li> testosterone (<a href="http://en.wikipedia.org/wiki/International_nonproprietary_name" target="_blank" title="International nonproprietary name in Wikipedia"><i>INN</i></a>) <br />
17β-hydroxyandrost-4-en-3-one (<i>fundamental parent + substitutive</i>) <br />
(1<i>S</i>,3a<i>S</i>,3b<i></i>R,9a<i>R</i>,9b<i>S</i>,11a<i>S</i>)-1-hydroxy-9a,11a-dimethyl-1,2,3,3a,3b,4,5,8,9,9a,9b,10,11,11a-tetradecahydro-7<i>H</i>-cyclopenta[<i>a</i>]phenanthren-7-one (<i>fused ring + additive + substitutive</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<a name='more'></a>
<p> We can try to name it systematically starting from the <a href="http://metallome.blogspot.com/2021/05/fused-ring-names.html" target="_blank" title="Fused ring names @ this blog">fused ring</a> parent hydride 1<i>H</i>-cyclopenta[<i>a</i>]phenanthrene <b>(b)</b>: </p>
<center>
<table>
<tbody><tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhPhVIi1jSjGFsfrgzQjm9cIOCbwKcpwDxlVq_34WrtzlxPFGD6OZEi7XwmKc1IM70BPDoT6sgt0z38YJF8eBD4UMngFFju5XrM8ObDymA6axMGyFuL_RL0Fq4r6yIIlgSyIM7wUH-R9CAX3sK3NKgSN3XRfuZllLI-Vp3-IVh1Ro_OvF44e8daQ/s500/1H-cyclopenta%5Ba%5Dphenanthrene.jpg" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1H-cyclopenta[a]phenanthrene"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhPhVIi1jSjGFsfrgzQjm9cIOCbwKcpwDxlVq_34WrtzlxPFGD6OZEi7XwmKc1IM70BPDoT6sgt0z38YJF8eBD4UMngFFju5XrM8ObDymA6axMGyFuL_RL0Fq4r6yIIlgSyIM7wUH-R9CAX3sK3NKgSN3XRfuZllLI-Vp3-IVh1Ro_OvF44e8daQ/w200-h200/1H-cyclopenta%5Ba%5Dphenanthrene.jpg" width="200" /></a></td></tr>
<tr><th align="center">(b)</th>
</tr></tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="2" type="a">
<li> 1<i>H</i>-cyclopenta[<i>a</i>]phenanthrene (<i>fused ring</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> The <a href="http://metallome.blogspot.com/2021/03/mancude-rings-and-annulenes.html" target="_blank" title="Mancude rings and annulenes @ this blog">mancude</a> structure <b>(b)</b> contains eight formal double carbon—carbon bonds while <b>(a)</b> has only one. To saturate seven double bonds of 1<i>H</i>-<span style="background-color: gold;">cyclopenta[<i>a</i>]phenanthren</span>e using organic <a href="http://metallome.blogspot.com/2020/09/additive-again.html" target="_blank" title="Additive again @ this blog">additive nomenclature</a> we need 14 hydrogens! That’s where the <span style="background-color: lightgreen;">tetradecahydro</span> bit is coming from. Substitution with –OH, two –CH<sub>3</sub>, and =O groups will give us <span style="background-color: lavender;">hydroxy</span>, <span style="background-color: lavender;">dimethyl</span> and <span style="background-color: lavender;">on</span>e, respectively. We furnish the name with locants and stereodescriptors to get the final product: (1<i>S</i>,3a<i>S</i>,3b<i></i>R,9a<i>R</i>,9b<i>S</i>,11a<i>S</i>)-1-<span style="background-color: lavender;">hydroxy</span>-9a,11a-<span style="background-color: lavender;">dimethyl</span>-1,2,3,3a,3b,4,5,8,9,9a,9b,10,11,11a-<span style="background-color: lightgreen;">tetradecahydro</span>-7<i>H</i>-<span style="background-color: gold;">cyclopenta[<i>a</i>]phenanthren</span>-7-<span style="background-color: lavender;">on</span>e. I bet you don’t like it<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. </p>
<p> Alternatively, we can base the name on the fully saturated parent hydride <b>(c)</b> called <a href="http://en.wikipedia.org/wiki/Androstane" target="_blank" title="Androstane in Wikipedia">androstane</a>:
</p>
<center>
<table>
<tbody><tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZpXhx4JhzvgCNw0tka7WR2ZBdA4SFMlEHm9518991_8OcYVjjnnuBRyLbFKdVh6LZlfxHCA-nMPD8ElVSlBEFVy7Gclf1M034JlvF2FxMS0AN1J9ghtE_FpoCwpQ6MtS6QtzLnQ2v11HgdLldMlDZsu8bOL9qoQJY4eCpK0n9Z5CjlpmSV8tqiA/s500/androstane.jpg" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="androstane"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZpXhx4JhzvgCNw0tka7WR2ZBdA4SFMlEHm9518991_8OcYVjjnnuBRyLbFKdVh6LZlfxHCA-nMPD8ElVSlBEFVy7Gclf1M034JlvF2FxMS0AN1J9ghtE_FpoCwpQ6MtS6QtzLnQ2v11HgdLldMlDZsu8bOL9qoQJY4eCpK0n9Z5CjlpmSV8tqiA/w200-h200/androstane.jpg" width="200" /></a></td></tr>
<tr><th align="center">(c)</th>
</tr></tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="3" type="a">
<li> androstane (<i>fundamental parent</i>) <br />
5ξ-androstane <br />
(3a<i>S</i>,3b<i>S</i>,5a<i>Ξ</i>,9a<i>S</i>,9b<i>S</i>,11a<i>S</i>)-9a,11a-dimethylhexadecahydro-1<i>H</i>-cyclopenta[<i>a</i>]phenanthrene (<i>fused ring + additive + substitutive</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> Note that the numbering of the structure <b>(c)</b> is totally different from that of <b>(b)</b>. </p>
<p> To insert a double bond at the position 4, we treat <span style="background-color: yellow;">androstan</span>e as we would any saturated hydrocarbon parent, viz. employing ‘an’ → ‘en’ operation. This will give us <span style="background-color: yellow;">androst</span>-4-<span style="background-color: wheat;">en</span>e. Substituting at the positions 3 and 17 with oxo and hydroxy groups, respectively, we get 17-<span style="background-color: lavender;">hydroxy</span><span style="background-color: yellow;">androst</span>-4-<span style="background-color: wheat;">en</span>-3-<span style="background-color: lavender;">on</span>e. </p>
<p> Now let’s look at the stereochemistry. The parent structure <b>(c)</b> has five chiral carbons; testosterone <b>(a)</b> has six. The extra chiral centre results from substitution by a hydroxy group at the position 17. Of course, we can mark its configuration as ‘<i>R</i>’ or ‘<i>S</i>’ according to the <a href="http://en.wikipedia.org/wiki/Cahn%E2%80%93Ingold%E2%80%93Prelog_priority_rules" target="_blank" title="Cahn–Ingold–Prelog priority rules in Wikipedia">Cahn–Ingold–Prelog</a> (CIP) rules. However, in the world of steroids and other natural products, it’s more common to use the α/β convention. </p>
<p> First, we have to make sure that the ring system in question is oriented in the standard way. The standard orientation of steroids is such that the cyclopentane ring of the cyclopenta[<i>a</i>]phenanthrene <b>(b)</b> skeleton appears in the top right part of the diagram [<a href="#Moss_1989" title="Moss (1989)">2</a>, <a href="http://iupac.qmul.ac.uk/steroid/3S01.html#3S14" target="_blank" title="Nomenclature of Steroids, 3S-1.4">3S-1.4</a>]. Now if an atom or group attached to the (properly oriented) ring system appears <i>below</i> it — that is, below the plane of the paper, or behind the plane of the computer screen displaying this structure — the configuration is denoted as ‘<a href="http://justsomesymbols.blogspot.com/2017/05/alpha.html" target="_blank" title="α | alpha @ just some symbols">α</a>’ (alpha); if the substituent is <i>above</i> this plane, the configuration is ‘<a href="http://justsomesymbols.blogspot.com/2017/05/beta.html" target="_blank" title="β | beta @ just some symbols">β</a>’ (beta)<sup><a href="#Footnote_†" title="Footnote †">†</a></sup>. In the case of <b>(a)</b>, the hydroxy group at C-17 is above the plane, so the full name will be 17β-<span style="background-color: lavender;">hydroxy</span><span style="background-color: yellow;">androst</span>-4-<span style="background-color: wheat;">en</span>-3-<span style="background-color: lavender;">on</span>e. </p>
<p> That’s better, isn’t it? Not only is this name significantly shorter, it’s also easier to interpret. Instead of listing <i>all</i> 14 positions where we add hydrogens, we specify merely <i>one</i> where we put the double bond. And, since the parent structure has five built-in chiral centres, we have to include only <i>one</i> stereodescriptor, not six. </p>
<p> This simplicity comes at a price though. We can’t deduce what ‘androstane’ is from first principles: we have to look it up. Moreover, to use the α/β notation correctly, we should know the standard orientation of the parent structure. For example, given the <a href="http://en.wikipedia.org/wiki/International_Chemical_Identifier" target="_blank" title="International Chemical Identifier in Wikipedia">InChI</a> or <a href="http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system" target="_blank" title="Simplified molecular-input line-entry system in Wikipedia">SMILES</a> string for <b>(c)</b>, we can regenerate the corresponding 2-D structure but there’s no guarantee it will be in a standard orientation. </p>
<p> Androstane is a fundamental parent structure, or <i>stereoparent</i> [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P10.html#101020103" target="_blank" title="Blue Book, P-101.2.1.3">P-101.2.1.3</a>]. IUPAC provides the <a href="http://iupac.qmul.ac.uk/BlueBook/P10.html#t1001" target="_blank" title="Blue Book, Table 10.1: Names of fundamental stereoparent structures">list</a> of recommended stereoparents and their <a href="http://iupac.qmul.ac.uk/BlueBook/Papp3.html" target="_blank" title="Blue Book, Appendix 3. Structures for Alkaloids, Steroids, Terpenoids and Similar Compounds">structures</a> in standard orientations [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P10.html#1010207" target="_blank" title="Blue Book, P-101.2.7">P-101.2.7</a>]. </p>
<p> The name ‘androstane’ implies the specific configurations of five chiral centres of <b>(c)</b>: 8β, 9α, 10β, 13β and 14α<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>. However, there is a sixth chiral atom, C-5. The α/β notation is used to specify the diastereomers 5α-androstane <b>(d)</b> and 5β-androstane <b>(e)</b>: </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28859" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="5α-androstane (CHEBI:28859)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKxLUJYlMBnsYFghZAvTMyKTELhchoWxkHY-rpvEdjcto83sn2wLEEb3v3qykNfZupKW_Sh8kVqNxr_6uuFErSwl1Z88ymY_XfXB3BmyTlX8kZcqdvoIRpIraVCs61heNEG7ToZ1dYRrtNC5w9Kcl5BhTqJH0hcNmDTFNxgfiK7gmwANe_UgTHrw/s1600/5-alpha-androstane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:20659" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="5β-androstane (CHEBI:20659)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjMTssd5jJDvEfrgUN_49DFO9NYiEZaY2JinXo56xcUbhpqapYvKXtyG-_lNWV1XG3ElNX5AZuw9q6ngwtJSTtCxksD8uMmGDVZRetGafxplFlF0VRNGLzuuloS8w9fmhacvQFWdIgahSnoJe58I-lL8PF4WsxSb2Nzwu3YkW9HrxZ-Ro2P-WB_Kw/s1600/5-beta-androstane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(d)</th> <th align="center">(e)</th></tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="4" type="a">
<li> 5α-androstane (<i>fundamental parent</i>) </li>
<li> 5β-androstane (<i>fundamental parent</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> To point out that the configuration of a chiral centre is unknown, the descriptor ‘<a href="http://justsomesymbols.blogspot.com/2017/05/xi.html" target="_blank" title="ξ | xi @ just some symbols">ξ</a>’ (xi) is used. Thus the structure <b>(c)</b> can be named 5ξ-androstane. Frankly, ‘ξ’ does not add much to the name but is a way to say “hey, we are <i>aware</i> that there is a chiral centre, we simply don’t know whether it’s ‘α’ or ‘β’”. </p>
<p> If configuration differs from that implied in the stereoparent, ‘α’ and ‘β’ are assigned to the corresponding chiral centres [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P10.html#101020601" target="_blank" title="Blue Book, P-101.2.6.1">P-101.2.6.1</a>]. </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:31527" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="dydrogesterone (CHEBI:31527)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhH8YRi1Gje80gqCVFnuxxf299jv8QJAxQ8CmyKiwNNcBQ4ZLnjUsRf1ljKLa71senQHoeX0ieCCGf_ogbRGl7z6t1hgMFViqfE3-zewFtpEkaoeLmIEDJnSr5UqxtBw9gLBG2xMTHkF6aoK2VjvfXAXX52L7bQ_g_UitgZRCvtIR90WqDOTjoD7w/s1600/dydrogesterone.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:8386" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="pregnane (CHEBI:8386)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiIuqDXYGRUScgRYvOyJARztCBcQwSaA_68_lacX13mLPELIdTLcAJNTjH7oXQT1S28tuIBcpIkkv6uHwvnMyfnOFbBAHqvbIwd9dl3rdUhfg2kbXGnmvdYIUyYmbQWSRMVo2eOT3mKcOiiNNrIBmwx0EQriIXDOXbTHt3DVWIoHEQB5AH2qI7bwA/s1600/pregnane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(f)</th> <th align="center">(g)</th></tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="6" type="a">
<li> dydrogesterone (<i>INN</i>) <br />
9β,10α-pregna-4,6-diene-3,20-dione (<i>fundamental parent + substitutive</i>) </li>
<li> pregnane (<i>fundamental parent</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> For instance, <a href="http://en.wikipedia.org/wiki/Dydrogesterone" target="_blank" title="Dydrogesterone in Wikipedia">dydrogesterone</a> <b>(f)</b> can be named semisystematically 9β,10α-<span style="background-color: yellow;">pregna</span>-4,6-<span style="background-color: wheat;">diene</span>-3,20-<span style="background-color: lavender;">dion</span>e. The ‘9β,10α’ bit indicates that the configurations of the C-9 and C-10 are inverted compared to the fundamental parent <span style="background-color: yellow;">pregnan</span>e <b>(g)</b>. </p>
<p> What if we need to invert <i>all</i> chiral centres in a molecule? Consider the structures <b>(h)</b> and <b>(i)</b>: </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36539" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="kaurane (CHEBI:36539)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQug7uUPL90dZY1G4CHvcJdzQOJxMpnMhuZMpM6nZlCDVWn3qVsPII32ffiSj2VWOGvFyXAewmytgr4CE0rx04b3Kze5XGGZ4wFSoSYr0rWHNTK8BL7aEWV6al4qz4rEoZ0yMLDnXuPHwBc_d7FekFt51sL8g02xjm2cg8Mqcd6tJbXqCGsaeFxw/s1600/kaurane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36540" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="ent-kaurane (CHEBI:36540)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXEO_JwIEvGcoCHhqGFNiOmKsqiVCq3mntEvasmppI5XEic_ju7u4A3u4ZujNBMil_6YF8fWlM0XJlSRvFRNi1wPLEgRPmE4qM73V4TEghwpErhdOnWbEdl18joahc-9E-pJLNpuvfv4IGH1ZpZenf_Q_xeCGVAzoQEV_lRaU-cExLOJwXwsa_8g/s1600/ent-kaurane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(h)</th> <th align="center">(i)</th></tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="8" type="a">
<li> kaurane (<i>fundamental parent</i>) </li>
<li> <i>ent</i>-kaurane (<i>fundamental parent</i>) <br />
(5β,8α,9β,10α,13α,16β)-kaurane (<i>fundamental parent</i>)
</li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> The compound <b>(h)</b> is a fundamental parent known as kaurane. For its enantiomer <b>(i)</b>, we can invert configurations at all chiral centres and name it (5β,8α,9β,10α,13α,16β)-kaurane. A shorter alternative is to call it <i>ent</i>-kaurane, with ‘<i>ent</i>’ being short for ‘enantio’ [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P10.html#1010801" target="_blank" title="Blue Book, P-101.8.1">P-101.8.1</a>].
</p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tbody><tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> Why, you might ask, we have ‘7<i>H</i>’ in (1<i>S</i>,3a<i>S</i>,3b<i></i>R,9a<i>R</i>,9b<i>S</i>,11a<i>S</i>)-1-<span style="background-color: lavender;">hydroxy</span>-9a,11a-<span style="background-color: lavender;">dimethyl</span>-1,2,3,3a,3b,4,5,8,9,9a,9b,10,11,11a-<span style="background-color: lightgreen;">tetradecahydro</span>-7<i>H</i>-<span style="background-color: gold;">cyclopenta[<i>a</i>]phenanthren</span>-7-<span style="background-color: lavender;">on</span>e <b>(a)</b> if the parent structure is 1<i>H</i>-<span style="background-color: gold;">cyclopenta[<i>a</i>]phenanthren</span>e and, moreover, the structure <b>(a)</b> has exactly zero hydrogens at the position 7? Well, there is a rule that dictates to put the <a href="http://goldbook.iupac.org/terms/view/I03004" target="_blank" title="indicated hydrogen in Gold Book">indicated hydrogens</a> at peripheral atoms that will host principal characteristic groups [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P5.html#58020301" target="_blank" title="Blue Book, P-58.2.3.1">P-58.2.3.1</a>]. In our case, we have the oxo group at C-7, so we move the indicated hydrogen there. It is as if we have started with a different tautomer of <b>(b)</b>, viz. 7<i>H</i>-<span style="background-color: gold;">cyclopenta[<i>a</i>]phenanthren</span>e:
<div class="separator" style="clear: both; text-align: center;"><p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9bov8oMpbFDAJoj04p5n9exgup9eRHG76yhbWVBcoCbyZ7Qxy0dDKceHTFDo6puBmIcVDKuFVCbuhJcyPYZu8isdgoBASt9_X5QHMNWfjvY3o1n3ecG0vSy6-aN69suAxINnWDCs4Dp3QYWZ_D95B28wloYJluoTbXQ5okIpetjSRmG_7DTVcCg/s500/7H-cyclopenta%5Ba%5Dphenanthrene.jpg" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="7H-cyclopenta[a]phenanthrene"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9bov8oMpbFDAJoj04p5n9exgup9eRHG76yhbWVBcoCbyZ7Qxy0dDKceHTFDo6puBmIcVDKuFVCbuhJcyPYZu8isdgoBASt9_X5QHMNWfjvY3o1n3ecG0vSy6-aN69suAxINnWDCs4Dp3QYWZ_D95B28wloYJluoTbXQ5okIpetjSRmG_7DTVcCg/w200-h200/7H-cyclopenta%5Ba%5Dphenanthrene.jpg" width="200" /></a></p></div>
Since we add hydrogens to all carbon atoms of the ring system except C-5 and C-5a (we keep the double bond between them) and C-7 (oxo group there), the resulting string of fourteen locants is ‘1,2,3,3a,3b,4,5,8,9,9a,9b,10,11,11a’. Cf. the systematic name for androstane <b>(c)</b>: (3a<i>S</i>,3b<i>S</i>,5a<i>Ξ</i>,9a<i>S</i>,9b<i>S</i>,11a<i>S</i>)-9a,11a-<span style="background-color: lavender;">dimethyl</span><span style="background-color: lightgreen;">hexadecahydro</span>-1<i>H</i>-<span style="background-color: gold;">cyclopenta[<i>a</i>]phenanthren</span>e. Here we start with 1<i>H</i>-<span style="background-color: gold;">cyclopenta[<i>a</i>]phenanthren</span>e and stay with ‘1<i>H</i>’. Because <b>(c)</b> is fully saturated, we don’t need any locants telling us <i>where</i> hydrogens are attached: just <span style="background-color: lightgreen;">hexadecahydro</span> is enough. The stereodescriptor ‘<i>Ξ</i>’ in ‘5a<i>Ξ</i>’ shows that the configuration at C-5a is not defined. </td></tr>
<tr><td valign="top">†</td>
<td> I find it counterintuitive to assign ‘β’ to the atom or group that is <i>closer</i> to the viewer. To English speakers, ‘α’ (<b>a</b>lpha) for <b>a</b>bove and ‘β’ (<b>b</b>eta) for <b>b</b>elow would make a really good mnemonic. </td></tr>
<tr><td valign="top">‡</td>
<td> The same is true for other steroid fundamental parents [<a href="#Moss_1989" title="Moss (1989)">2</a>, <a href="http://iupac.qmul.ac.uk/steroid/3S01.html#3S15" target="_blank" title="Nomenclature of Steroids, 3S-1.5">3S-1.5</a>]. </td>
</tr>
</tbody></table>
<h4>References</h4>
<ol>
<a name="Blue_Book_2014"></a>
<li>Favre, H.A. and Powell, W.H. <a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
<a name="Moss_1989"></a>
<li> Moss, G.P. (1989) Nomenclature of steroids (Recommendations 1989). <a href="http://doi.org/10.1351/pac198961101783" target="_blank" title="Moss (1989) Pure Appl. Chem. 61, 1783-1822."><i>Pure and Applied Chemistry</i> <b>61</b>, 1783—1822</a>.
</li></ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-19185933076584657232024-02-12T12:00:00.022+00:002024-02-24T11:49:44.333+00:00Planar chirality<p> In most organic chemistry textbooks, double bond <a href="http://metallome.blogspot.com/2023/09/cis-and-trans.html" target="_blank" title="cis and trans @ this blog"><i>cis</i>/<i>trans</i> isomerism</a> is exemplified by alkenes. It is also observed in <a href="http://metallome.blogspot.com/2021/03/alicyclic-monocycles.html" target="_blank" title="Alicyclic monocycles @ this blog">cycloalkenes</a> such as <a href="http://en.wikipedia.org/wiki/Cyclooctene" target="_blank" title="Cyclooctene in Wikipedia">cyclooctene</a> that can exist as either <i>cis</i> <b>(a)</b> or <i>trans</i> <b>(b)</b> isomer: </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:225365" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cis-cyclooctene (CHEBI:225365)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqA8A9X900YqM4niuJ9EwqUMJ9OaPepK1cW-V4ZNW54bl7E-pJOmu1kx9hOTWFZ7syw4vZUwriDXo1KOKO5lmO5rDjKuPXAxcw22K0WrRWI0mXLUBc1eSoLUeWmFd2eqUO0t3ALg6KeQW78kDftFOjYYcl_TLSwvCMrNoKcYrKNNRKofoom_r6mQ/s1600/cis-cyclooctene.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:73156" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="trans-cyclooctene (CHEBI:73156)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBaK5otPnkC9YgVbD9JoiHjRcHmqQD7c5l2AU64nv8X6dHjHwooCS6HDqn5TDOE8NF6kUJo9aoOZidRgHXlHGS-o-g-qI1x7X-ddgqp-C_I_gAIjQKrpqSXGm1Q66W93QgPDoPa65RS0OQo8Z1IrheDFRIbYT9nO15BN_Qc3DyA3OGJvpT9VACUg/s1600/trans-cyclooctene.png" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> (<i>Z</i>)-cyclooctene (<i><a href="http://en.wikipedia.org/wiki/Preferred_IUPAC_name" target="_blank" title="Preferred IUPAC name in Wikipedia">PIN</a></i>) <br />
<i>cis</i>-cyclooctene </li>
<li> (<i>E</i>)-cyclooctene (<i>PIN</i>) <br />
<i>trans</i>-cyclooctene </li>
</ol>
</td></tr>
</table>
</center>
<p> To the <i>trans</i> isomer, there is a twist — and the pun is fully intended. Have a look at the structures <b>(c)</b> and <b>(d)</b> (or at their 3-D models <a href="http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RS14272/planar.html#dioxa55" target="_blank" title="Planar Chirality: (E)-Cyclooctene @ Organic Chemistry (Chemistry 220), Yale University">here</a>, <a href="http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/isomers/RS14272/planar.html#dioxa55" target="_blank" title="Planar Chirality: (E)-Cyclooctene @ Organic Chemistry (Chemistry 220), Yale University">Fig. 2 and Fig. 3</a>, respectively). </p>
<center>
<table>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJZu7M_uFspjCgXYF0KVOTXO9pkYaTO0mA-7DJvCovDPyiKMX4VdyiV_jaQ9qAt9ZtquvgQcMlFOpmf5gEjBdGZuRnOFsjF6-REqedArPuQQSD2s9dnVuddmSKQaKjiI82oE2U8-vbop3Q7u8bEmObuYCupkHMa9aQs7AS6gqV_q9rK7mvJBn21g/s500/(E,P)-cyclooctene.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJZu7M_uFspjCgXYF0KVOTXO9pkYaTO0mA-7DJvCovDPyiKMX4VdyiV_jaQ9qAt9ZtquvgQcMlFOpmf5gEjBdGZuRnOFsjF6-REqedArPuQQSD2s9dnVuddmSKQaKjiI82oE2U8-vbop3Q7u8bEmObuYCupkHMa9aQs7AS6gqV_q9rK7mvJBn21g/w200-h200/(E,P)-cyclooctene.jpg" width="200" /></a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF2YOzWJ6CbiNxOP38K9abG2louMUSdbWlmZSQsZj1CQ2CiaLQCvRW1bTD4jRALwPajYC07oJaJ7yF-9dGypUXNNWKESLh0bJIQOqzicQU4BRwMBOYmExFU2BBIsaO_-76xGZ68wVy4WWHDbmJ3C3fKYLfkW051CvCT5WPEBkvBKjkId56ZuJxFA/s500/(E,M)-cyclooctene.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF2YOzWJ6CbiNxOP38K9abG2louMUSdbWlmZSQsZj1CQ2CiaLQCvRW1bTD4jRALwPajYC07oJaJ7yF-9dGypUXNNWKESLh0bJIQOqzicQU4BRwMBOYmExFU2BBIsaO_-76xGZ68wVy4WWHDbmJ3C3fKYLfkW051CvCT5WPEBkvBKjkId56ZuJxFA/w200-h200/(E,M)-cyclooctene.jpg" width="200" /></a></td></tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> (1<i>E</i>,1<i>P</i>)-cyclooct-1-ene (<i>PIN</i>) <br />
(<i>E</i>,<i>P</i>)-cyclooctene <br />
(<i>E</i>,<i>R</i><sub>p</sub>)-cyclooctene </li>
<li> (1<i>E</i>,1<i>M</i>)-cyclooct-1-ene (<i>PIN</i>) <br />
(<i>E</i>,<i>M</i>)-cyclooctene <br />
(<i>E</i>,<i>S</i><sub>p</sub>)-cyclooctene </li>
</ol>
</td></tr>
</table>
</center>
<a name='more'></a>
<p> Isn’t it obvious that <b>(c)</b> and <b>(d)</b> are a pair of enantiomers? Like it is the case with <a href="http://metallome.blogspot.com/2023/12/axial-chirality.html" target="_blank" title="Axial chirality @ this blog">axially chiral compounds</a>, the molecules <b>(c)</b> and <b>(d)</b> do not have any chiral centre. What’s more, they also lack a chiral axis! What we have here is an example of <a href="http://en.wikipedia.org/wiki/Planar_chirality" target="_blank" title="Planar chirality in Wikipedia">planar chirality</a>, which the <a href="http://goldbook.iupac.org/terms/view/P04681" target="_blank" title="planar chirality in Gold Book">Gold Book</a> not-quite-defines as </p>
<blockquote> Term used by some authorities to refer to stereoisomerism resulting from the arrangement of out-of-plane groups with respect to a plane (<a href="http://goldbook.iupac.org/terms/view/C01062" target="_blank" title="chirality plane in Gold Book">chirality plane</a>). </blockquote>
<p> “Some authorities”? It’s as if IUPAC doesn’t want to have anything to do with those anonymous authorities. Luckily, the Blue Book assumes a bit of responsibility modifying the above definition thus [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9201020103" target="_blank" title="Blue Book, P-92.1.2.1.3">P-92.1.2.1.3</a>]: </p>
<blockquote> Planar chirality is a term used to refer to stereoisomerism resulting from the arrangement of out of plane groups with respect to a plane (stereogenic plane). </blockquote>
<p> To specify the configuration of the molecules with planar chirality, the stereodescriptors ‘<i>R</i><sub>p</sub>’ and ‘<i>S</i><sub>p</sub>’<sup><a href="#Footnote_*" title="Footnote *">*</a></sup> or ‘<i>M</i>’ and ‘<i>P</i>’ are employed, with the latter pair being preferred by IUPAC. Although the Blue Book uses <i>trans</i>-cyclooctene to illustrate planar chirality, it does not explain very well <i>how</i> these descriptors are assigned to the enantiomers [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9305010401" target="_blank" title="Blue Book, P-93.5.1.4.1">P-93.5.1.4.1</a>]. Let’s see if I can do it better. </p>
<p> I find it much easier to think of a <i>part</i> of cyclooctene as a helix. Focus on the chain –HC=CH–CH<sub>2</sub>–CH<sub>2</sub>–, that is, carbon atoms C-1 through C-4. The carbons C-1 and C-2 are trigonal planar (<i>TP</i>-3), which means that the hydrogens attached to C-1 and C-2, as well as C-3 (and also C-8) are all in the same plane. This is our <i>chirality plane</i>. In the structure <b>(c)</b>, if we look at this plane from the side of the ring, we’ll see the path from C-1 to C-2 to C-3 going <i>clockwise</i> (↻) before plunging down to C-4. Just like a right-handed helix would do. So this structure is the ‘<i>P</i>’ (“plus”) isomer. Conversely, in <b>(d)</b> the path C-1 → C-2 → C-3 goes <i>anticlockwise</i> (↺), so it’s the ‘<i>M</i>’ (“minus”) isomer. </p>
<p> Still sounds too complicated? I have an easier method. Take a piece of paper (A5 will do). Hold it with two hands in front of you. Now turn either hand clockwise (↻). What you have in your hands now looks like the structure <b>(c)</b>, that is, the ‘<i>P</i>’ isomer, right? Anticlockwise (↺) — ‘<i>M</i>’ isomer <b>(d)</b>. </p>
<p> The preferred IUPAC names for <b>(c)</b> and <b>(d)</b> will be (1<i>E</i>,1<i>P</i>)-cyclooct-1-ene and (1<i>E</i>,1<i>M</i>)-cyclooct-1-ene, respectively. <a name="do_we_really_need_locant"></a> Do we really need locant ‘1’ if there is only one double bond and, accordingly, only one chirality plane? No we don’t: (<i>E</i>,<i>P</i>)-cyclooctene and (<i>E</i>,<i>M</i>)-cyclooctene are completely unambiguous. </p>
<p> <a href="http://en.wikipedia.org/wiki/(2.2)Paracyclophane" target="_blank" title="[2.2]Paracyclophane in Wikipedia">Paracyclophanes</a> are another class of structures exhibiting planar chirality. Observe the enantiomers <b>(e)</b> and <b>(f)</b>: </p>
<center>
<table>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5PLiZ35k1ug_bBp4Q9s_N1GXsIqMhPD_T_K9TfES5QEfxmMwSB0XPaJOAguNhBgzpkj3-yEAWHugbwpPOh8K1N1UHbrMOGnbVuOpyl3RSUoE6u1IWkJ3ZDoXVFf5S-Vtrq3enLY_IFWiELapJ4vAFkF1Wwv_x5_g3O-X6b0nRMmHv2nm7AZwtxw/s500/(P)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5PLiZ35k1ug_bBp4Q9s_N1GXsIqMhPD_T_K9TfES5QEfxmMwSB0XPaJOAguNhBgzpkj3-yEAWHugbwpPOh8K1N1UHbrMOGnbVuOpyl3RSUoE6u1IWkJ3ZDoXVFf5S-Vtrq3enLY_IFWiELapJ4vAFkF1Wwv_x5_g3O-X6b0nRMmHv2nm7AZwtxw/w200-h200/(P)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane.jpg" width="200" /></a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYbNfRr16RQOKwy3l406rF9iTiWQX2EZAXEVvVwX8f6Ce7b1At8jR8MgWp6xA0c9dzARPjPIE24ix7gYodJqxQgw4YOP0Wxl59eGw5E4vHT3FTlwWZiF9v8BoPcIsBmi02GBzIGeMoJ98TiJqsxrFMT89NhM5LQZ5r4PO2OyoRriHWrSRW2dDZ7A/s500/(M)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYbNfRr16RQOKwy3l406rF9iTiWQX2EZAXEVvVwX8f6Ce7b1At8jR8MgWp6xA0c9dzARPjPIE24ix7gYodJqxQgw4YOP0Wxl59eGw5E4vHT3FTlwWZiF9v8BoPcIsBmi02GBzIGeMoJ98TiJqsxrFMT89NhM5LQZ5r4PO2OyoRriHWrSRW2dDZ7A/w200-h200/(M)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane.jpg" width="200" /></a></td>
</tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th></tr>
</table>
</center>
<p> We can name them systematically using <a href="http://metallome.blogspot.com/2021/11/phane-names.html" target="_blank" title="Phane names @ this blog">phane nomenclature</a>. Let’s refresh how it’s done. But first, I have to clutter the diagrams some more with locants: </p>
<center>
<table>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibgIvlhqZjTomBXi_zuw-hGznXMZHTkDHOUKDeOiqmSv6BxUGeBFkB3YbwfG9KJVhicbAvivs4l888C0cyNd1nJnJJdKt-fD2snvY-A_RvDlHd7G0dW6v2t8m-wTtbI2YnGEQri7YQvq1ymBEOUvSCOmYAn8i5kVyot3sSemwxik9Li2p-mxYT3Q/s500/(P)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane_numbered.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibgIvlhqZjTomBXi_zuw-hGznXMZHTkDHOUKDeOiqmSv6BxUGeBFkB3YbwfG9KJVhicbAvivs4l888C0cyNd1nJnJJdKt-fD2snvY-A_RvDlHd7G0dW6v2t8m-wTtbI2YnGEQri7YQvq1ymBEOUvSCOmYAn8i5kVyot3sSemwxik9Li2p-mxYT3Q/w200-h200/(P)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane_numbered.jpg" width="200" /></a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiH4Fb6cHkL5lp-Tm_WguTbxksk06uDdnRgKN5XsMnLMswQ35aZupI60JeCO10ebkEfQ53ajL_B-L5wCwVE7Rx_JzYIfGK20GxwJr3_2T6Z7PFvSaXXJsoVV3P1SmtnQCS9_LoQ-ZeHYung8LfOHx_0VFbhSrLXn2eCR-WtDTRso2Aq0jhKiQSeyw/s500/(M)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane_numbered.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiH4Fb6cHkL5lp-Tm_WguTbxksk06uDdnRgKN5XsMnLMswQ35aZupI60JeCO10ebkEfQ53ajL_B-L5wCwVE7Rx_JzYIfGK20GxwJr3_2T6Z7PFvSaXXJsoVV3P1SmtnQCS9_LoQ-ZeHYung8LfOHx_0VFbhSrLXn2eCR-WtDTRso2Aq0jhKiQSeyw/w200-h200/(M)-1.2-iodo-1,4(1,4)-dibenzenacyclohexaphane_numbered.jpg" width="200" /></a></td>
</tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> (1<sup>1</sup><i>P</i>)-1<sup>2</sup>-iodo-1,4(1,4)-dibenzenacyclohexaphane (<i>phane + substitutive, PIN</i>) <br />
(1<sup>1</sup><i>R</i><sub>p</sub>)-1<sup>2</sup>-iodo-1,4(1,4)-dibenzenacyclohexaphane (<i>phane + substitutive</i>) </li>
<li> (1<sup>1</sup><i>M</i>)-1<sup>2</sup>-iodo-1,4(1,4)-dibenzenacyclohexaphane (<i>phane + substitutive, PIN</i>) <br />
(1<sup>1</sup><i>S</i><sub>p</sub>)-1<sup>2</sup>-iodo-1,4(1,4)-dibenzenacyclohexaphane (<i>phane + substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> The name is based on a “simplified skeletal name”, which is <span style="background-color: yellow;">cyclohexane</span>, modified to contain ‘phane’, i.e. <span style="background-color: yellow;">cyclohexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. Adding the locants for superatoms <b>1</b> and <b>4</b> gives us 1,4-di<span style="background-color: yellow;">cyclohexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. Replacing the superatoms <b>1</b> and <b>4</b> with <span style="background-color: palegreen;">benzene</span> rings, we get 1,4-di<span style="background-color: palegreen;">benzena</span><span style="background-color: yellow;">cyclohexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. Specifying that the benzene rings are attached at positions 1 and 4, we add these locants in parentheses following the superatom locants: 1,4(1,4)-di<span style="background-color: palegreen;">benzena</span><span style="background-color: yellow;">cyclohexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. Substututing the first benzene ring at the second position (i.e. 1<sup>2</sup>) by <span style="background-color: lavender;">iodine</span> results in 1<sup>2</sup>-<span style="background-color: lavender;">iodo</span>-1,4(1,4)-di<span style="background-color: palegreen;">benzena</span><span style="background-color: yellow;">cyclohexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span><sup><a href="#Footnote_†" title="Footnote †">†</a></sup>. </p>
<p> This is all fine, I hear, what’s about chirality? According to the Blue Book, the configuration is indicated by the stereodescriptors ‘<i>R</i><sub>p</sub>’ and ‘<i>S</i><sub>p</sub>’ assigned to the carbon C-1<sup>1</sup> [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9201020103" target="_blank" title="Blue Book, P-92.1.2.1.3">P-92.1.2.1.3</a>]. The explanation involves a tetrahedron whose base is formed by the three atoms attached to C-1<sup>1</sup>. I appreciate organic chemists’ love of tetrahedra, however here it does not help much. Elsewhere, a different and slightly more transparent exposition is given for the descriptors ‘<i>P</i>’ and ‘<i>M</i>’ [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9201020202" target="_blank" title="Blue Book, P-92.1.2.2.2">P-92.1.2.2.2</a>]. Yet another run-down on stereogenic planes invokes the “pilot atom”, never defined and never mentioned again [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93050501" target="_blank" title="Blue Book, P-93.5.5.1">P-93.5.5.1</a>]. Can’t we assign the helicity descriptors ‘<i>P</i>’ and ‘<i>M</i>’, once again, using a helix? Let me have a go. </p>
<p> Our chirality plane is the one of the benzene ring <b>1</b>. All its carbon atoms, as well as the atoms attached to them — that is, hydrogens, iodine, and carbon C-2 — are in the same plane. We start from C-1<sup>2</sup> (and not from C-1<sup>6</sup>) because it is the highest priority carbon atom according to the <a href="http://en.wikipedia.org/wiki/Cahn%E2%80%93Ingold%E2%80%93Prelog_priority_rules" target="_blank" title="Cahn–Ingold–Prelog priority rules in Wikipedia">Cahn–Ingold–Prelog</a> (CIP) rules. In the structure <b>(e)</b>, the path from C-1<sup>2</sup> to C-1<sup>1</sup> to C-2 is going clockwise (↻) before heading down to C-3. Just like a right-handed helix. So <b>(e)</b> is the ‘<i>P</i>’ isomer and the complete name will be (1<sup>1</sup><i>P</i>)-1<sup>2</sup>-<span style="background-color: lavender;">iodo</span>-1,4(1,4)-di<span style="background-color: palegreen;">benzena</span><span style="background-color: yellow;">cyclohexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. On the other hand (literally), in <b>(f)</b> the path C-1<sup>2</sup> → C-1<sup>1</sup> → C-2 goes <i>anticlockwise</i> (↺), so it’s the ‘<i>M</i>’ isomer. Easy? Easy. </p>
<p> Looking at the PINs, one can feel somehow uncomfortable that, in spite of not having a chiral centre, the ‘<i>P</i>’ and ‘<i>M</i>’ descriptors have to be attached to a particular atom: C-1 in <b>(c)</b> and <b>(d)</b>, C-1<sup>1</sup> in <b>(e)</b> and <b>(f)</b>. I don’t think there’s any pressing need to <a href="#do_we_really_need_locant" title="do we really need to specify the locant in cyclooctene?">specify the locant in cyclooctene</a>. This is not the case with paracyclophanes where <i>each</i> ring can have its own planar chirality, as shown in [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93050501" target="_blank" title="Blue Book, P-93.5.5.1">P-93.5.5.1</a>]. If I had my way, I would replace ‘(1<sup>1</sup><i>P</i>)’ and ‘(1<sup>1</sup><i>M</i>)’ with ‘(1<i>P</i>)’ and ‘(1<i>M</i>)’, respectively, for it is more logical to attach the descriptor to the whole ring <b>1</b> than just to the atom C-1<sup>1</sup>. </p>
<p> Given that IUPAC prefers the descriptors ‘<i>P</i>’ and ‘<i>M</i>’ to ‘<i>R</i><sub>a</sub>’ and ‘<i>S</i><sub>a</sub>’ as well as to ‘<i>R</i><sub>p</sub>’ and ‘<i>S</i><sub>p</sub>’, one can feel that there is reluctance to bring the notions of axial and planar chirality into the systematic names. Constable [<a href="#Constable_2021" title="Constable (2021)">3</a>] points out that the structures like biaryls can be described either as axially or planar chiral. For instance, the same ‘<i>P</i>’ biaryl isomer will be assigned either ‘<i>S</i><sub>a</sub>’ or ‘<i>R</i><sub>p</sub>’ descriptor. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> Like with ‘<i>R</i><sub>a</sub>’ and ‘<i>S</i><sub>a</sub>’, it is not clear how the descriptors ‘<i>R</i><sub>p</sub>’ and ‘<i>S</i><sub>p</sub>’ are meant to be <i>pronounced</i>. “<i>R</i> planar” and “<i>S</i> planar” sound more Spanish than English because the adjective “planar” follows the descriptor. On the other hand, in Spanish chemical literature you’ll find the descriptors ‘<sub>p</sub><i>R</i>’ and ‘<sub>p</sub><i>S</i>’ [<a href="#Quiroga_Feijoo_2007" title="Quiroga Feijóo (1968)">2</a>, p. 127]. </td></tr>
<tr><td valign="top">†</td>
<td> If you think this name is long or clumsy, check out its <a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog">von Baeyer</a> alternative: 5-iodotricyclo[8.2.2.2<sup>4,7</sup>]hexadeca-1(12),4,6,10,13,15-hexaene. Of course, the atom numbering here is totally different to that in <b>(e)</b>/<b>(f)</b>.
<div class="separator" style="clear: both; text-align: center;"><p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXXrLP7wSZobFdX9n-IFFXrV1kQ0runV7QkmdMK_J2n3j3oxN-rN2JtqABd0pXRoqSafhSnqLplelhmUxI_b4nz6MzL4Qy_jLywTC7E5Po-_UmsBLGOUKqvRYHPb55Kjm2mGyk4thUK4zFFsx47dOWwI8VEPTUzQEYHqjN2buDowvjnhuEYk4mKA/s500/5-iodotricyclo%5B8.2.2.2(4,7)%5Dhexadeca-1(12),4,6,10,13,15-hexaene.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXXrLP7wSZobFdX9n-IFFXrV1kQ0runV7QkmdMK_J2n3j3oxN-rN2JtqABd0pXRoqSafhSnqLplelhmUxI_b4nz6MzL4Qy_jLywTC7E5Po-_UmsBLGOUKqvRYHPb55Kjm2mGyk4thUK4zFFsx47dOWwI8VEPTUzQEYHqjN2buDowvjnhuEYk4mKA/w200-h200/5-iodotricyclo%5B8.2.2.2(4,7)%5Dhexadeca-1(12),4,6,10,13,15-hexaene.jpg" width="200" /></a></p></div>
</td></tr>
</table>
<h4>References</h4>
<ol>
<a name="Blue_Book_2014"></a>
<li>Favre, H.A. and Powell, W.H. <a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
<a name="Quiroga_Feijoo_2007"></a>
<li> Quiroga Feijóo, M.L. <a href="https://amzn.to/3SaZccP" target="_blank" title="Estereoquímica @ Amazon.co.uk"><i>Estereoquímica: conceptos y aplicaciones en química orgánica</i></a>. Editorial Síntesis, Madrid, 2007. </li>
<a name="Constable_2021"></a>
<li> Constable, E.C. (2021) Through a glass darkly — Some thoughts on symmetry and chemistry. <a href="http://doi.org/10.3390/sym13101891" target="_blank" title="Constable (2021) Symmetry 13, 1891."><i>Symmetry</i> <b>13</b>, 1891</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-42913509029196541822023-12-10T21:00:00.035+00:002024-02-24T11:46:50.734+00:00Axial chirality<p> Have a look at the structures <b>(a)</b> and <b>(b)</b>. They are the stereoisomers of <a href="http://de.wikipedia.org/wiki/Laballens%C3%A4ure" target="_blank" title="Laballensäure in German Wikipedia">laballenic acid</a>, with <b>(a)</b> is naturally occurring in plants of the <a href="http://en.wikipedia.org/wiki/Lamiaceae" target="_blank" title="Lamiaceae in Wikipedia">Lamiaceae</a> family. What kind of stereoisomers are they? </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:38401" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(R)-laballenic acid (CHEBI:38401)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbzThzmGgu0wYywFeRY04dir3rdBVjIEBcfermsfEXHt0bGjqT7Uj7l3o_py-2adaAWZytZA0sXq_TUO2w1xol8DBPQ5eVSUz_Q5LOwtleHhIVHfV6PjNcxtl7spQ_DvoyFppW3BqwBsQciwIDuDfjt4T3w3vbHLvrszbQ1oPfyitcxXysK7008w/s1600/(R)-laballenic_acid.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:38402" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(S)-laballenic acid (CHEBI:38402)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEic1vtXq6AHGFaCc0U19n5RWhrINp4tY1l_iQQdEIq9p33ENxpJmOO7oJdRevR2ZDe6ttIHLnjV8jB7eXV8rk9i9bhEExMy5EvagIABuQ68Hb0g_26c9QKoRv1tpgpQPCaX0yh840hkNOpoX8081Dh4vY_F02EntCmiUvUKzbeGfnrz6Ey0DSkRwg/s1600/(S)-laballenic_acid.png" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> (−)-laballenic acid (<i>trivial</i>) <br />
(5<i>M</i>)-octadeca-5,6-dienoic acid (<i>substitutive, <a href="http://en.wikipedia.org/wiki/Preferred_IUPAC_name" target="_blank" title="Preferred IUPAC name in Wikipedia">PIN</a></i>) <br />
(5<i>R</i><sub>a</sub>)-octadeca-5,6-dienoic acid (<i>substitutive</i>) </li>
<li> (+)-laballenic acid (<i>trivial</i>) <br />
(5<i>P</i>)-octadeca-5,6-dienoic acid (<i>substitutive, PIN</i>) <br />
(5<i>S</i><sub>a</sub>)-octadeca-5,6-dienoic acid (<i>substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> If there was just one double bond in the middle of the molecule, we’ll be dealing with <a href="http://metallome.blogspot.com/2023/09/cis-and-trans.html" target="_blank" title="cis and trans @ this blog"><i>cis</i>/<i>trans</i> isomerism</a>. But we have <i>two</i> <a href="http://goldbook.iupac.org/terms/view/C01437" target="_blank" title="cumulative double bonds in Gold Book">cumulative double bonds</a>, which makes our molecules chiral, even though there are no <i>chiral atoms</i>. Why? </p>
<a name='more'></a>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37602" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="allenes (CHEBI:37602)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqRJxS-wq6XaPnfWEJqxpbrNiLVnKukEg1A7jUT3XuroMKeRT8rkg_b2o8KsdFLsU1M8Czf7oLCUxKXaHlgmMfDvQVjumBDwE_FgbRzgZcBoiBu9112BHI2FLYvn7kwoCcrjzzTzqJANGs3JPu-e9MwXm5Db7VPKPjK9di8itfculILarMLTXhQw/s1600/allenes.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th> </tr>
</table>
</center>
<p> The diagram <b>(c)</b> represents a generic <a href="http://en.wikipedia.org/wiki/Allenes" target="_blank" title="Allenes in Wikipedia">allene</a> structure. The central carbon atom has linear geometry (<i>L</i>-2); it is linked by double bonds to the trigonal planar (<i>TP</i>-3) carbon atoms. The whole structure, however, could be thought of as an elongated tetrahedron with vertices R1, R2, R3 and R4. Structures like that are said to have <a href="http://goldbook.iupac.org/terms/view/A00547" target="_blank" title="axial chirality in Gold Book"><i>axial chirality</i></a>. For an allene to be chiral (that is, not superposable on its mirror image), there’s no need to have four different substituents: that R1 ≠ R2 and R3 ≠ R4 will suffice. In <b>(c)</b>, the <a href="http://goldbook.iupac.org/terms/view/C01059" target="_blank" title="chirality axis in Gold Book"><i>chirality axis</i></a> goes along the C=C=C bonds and the planes C(R1)(R2) and C(R3)(R4) are at 90° to each other. So <b>(a)</b> and <b>(b)</b> are <a href="http://metallome.blogspot.com/2023/09/enantiomers.html" target="_blank" title="Enantiomers @ this blog">enantiomers</a>. </p>
<p> To specify the configuration of the molecules with axial chirality, the stereodescriptors ‘<i>R</i><sub>a</sub>’ and ‘<i>S</i><sub>a</sub>’ or ‘<i>M</i>’ and ‘<i>P</i>’ are used, with the latter convention being preferred by IUPAC [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93040202" target="_blank" title="Blue Book, P-93.4.2.2">P-93.4.2.2</a>]. We assign the priorities within each pair of substituents, viz. (R1, R2) and (R3, R4), according to the <a href="http://en.wikipedia.org/wiki/Cahn%E2%80%93Ingold%E2%80%93Prelog_priority_rules" target="_blank" title="Cahn–Ingold–Prelog priority rules in Wikipedia">Cahn–Ingold–Prelog</a> (CIP) sequence rules. As a result, we’ll have two axes, let’s call them <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①–②</span> and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′–②′</span>. If we look at the molecule along the chirality axis, we’ll see <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①–②</span> perpendicular to <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′–②′</span>. Now we can use either of two methods: </p>
<a name="PM_convention"></a>
<ul>
<li> <i>P</i>/<i>M</i> convention [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9201020201" target="_blank" title="Blue Book, P-92.1.2.2.1">P-92.1.2.2.1</a>]: if the sequence <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①–①′</span> (or <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′–①</span>, it doesn’t matter from which end you look) goes <i>clockwise</i>, it’s denoted by the ‘<i>P</i>’ (“plus”) stereodescriptor; if <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①–①′</span> goes <i>anticlockwise</i>, it gets ‘<i>M</i>’ (“minus”). </li>
<li> <i>R</i><sub>a</sub>/<i>S</i><sub>a</sub> convention [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9201020102" target="_blank" title="Blue Book, P-92.1.2.1.2">P-92.1.2.1.2</a>]: if the sequence <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①–②–①′</span> (or <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′–②′–①</span>) goes <i>clockwise</i>, it’s ‘<i>R</i><sub>a</sub>’ (that is, “axial” <i>R</i>); otherwise — i.e. <i>anticlockwise</i> — it’s ‘<i>S</i><sub>a</sub>’ (“axial” <i>S</i>)<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. </li>
</ul>
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf1iMT3g7GCNaGh_MUUQlCnmeh0sFN_reMmVEDXr37si-7u5yeQ5WP2sC2jFEhJzvfVgsbP9H7SHFAFbfQr57UQ03FSTazcpUEmRrIQ9LgWvK2OkFZVNPqLA_gJA4U9pgoLBME8-NTQP2MWnjDTcFvwQdPk1_b89YL461_SKe0lkRqUS8wJxn9ng/s1057/MPRaSa.png" style="margin-left: 1em; margin-right: 1em;" title="Comparison of P/M (green) and Ra/Sa (orange) conventions"><img border="0" data-original-height="595" data-original-width="1057" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf1iMT3g7GCNaGh_MUUQlCnmeh0sFN_reMmVEDXr37si-7u5yeQ5WP2sC2jFEhJzvfVgsbP9H7SHFAFbfQr57UQ03FSTazcpUEmRrIQ9LgWvK2OkFZVNPqLA_gJA4U9pgoLBME8-NTQP2MWnjDTcFvwQdPk1_b89YL461_SKe0lkRqUS8wJxn9ng/w400-h225/MPRaSa.png" width="400" /></a></div>
<p> As you can see, ‘<i>R</i><sub>a</sub>’ corresponds to ‘<i>M</i>’ and ‘<i>S</i><sub>a</sub>’ to ‘<i>P</i>’. Therefore, we name <b>(a)</b> as either (5<i>M</i>)-octadeca-5,6-dienoic acid (PIN) or (5<i>R</i><sub>a</sub>)-octadeca-5,6-dienoic acid, and <b>(b)</b> (5<i>P</i>)-octadeca-5,6-dienoic acid (PIN) or (5<i>S</i><sub>a</sub>)-octadeca-5,6-dienoic acid. </p>
<p> One of the advantages of <i>M</i>/<i>P</i> system over the <i>R</i><sub>a</sub>/<i>S</i><sub>a</sub> can be demonstrated on the example of <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:177873" target="_blank" title="grasshopper ketone (CHEBI:177873)">grasshopper ketone</a> <b>(d)</b><sup><a href="#Footnote_†" title="Footnote †">†</a></sup>. In its systematic name, (3<i>M</i>)-4-[(2<i>R</i>,4<i>S</i>)-2,4-dihydroxy-2,6,6-trimethylcyclohexylidene]but-3-en-2-one, the stereodescriptor ‘<i>M</i>’ is easily distinguishable from the “real tetrahedral” descriptors ‘<i>R</i>’ and ‘<i>S</i>’. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:177873" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="grasshopper ketone (CHEBI:177873)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7NZYYociF_gvPzk3fRhsuC1tcJDTi6f8B8-gdA3myxljSH3q-M6SHjnq0sG_7pzgwkuJr_E4VdSDSME61rAdtyk_bRbNh5y8JyQighmOXmNN2eIDzOkVBZHYaJMS2WQFZWysvft-5xClQ7p3X_YWCJLD8sgC1Fq-lEtjfc15mj0VplPuCrqEYpQ/s1600/grasshopper_ketone.png" width="200" /></a></td></tr>
<tr><th align="center">(d)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="4" type="a">
<li> grasshopper ketone (<i>trivial</i>) <br />
(3<i>M</i>)-4-[(2<i>R</i>,4<i>S</i>)-2,4-dihydroxy-2,6,6-trimethylcyclohexylidene]but-3-en-2-one (<i>substitutive, PIN</i>) <br />
(3<i>R</i><sub>a</sub>)-4-[(2<i>R</i>,4<i>S</i>)-2,4-dihydroxy-2,6,6-trimethylcyclohexylidene]but-3-en-2-one (<i>substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> Apart from molecules with an even number of cumulative double bonds [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93040202" target="_blank" title="Blue Book, P-93.4.2.2">P-93.4.2.2</a>], there are other classes of compounds that show axial chirality. Among them, <a href="http://goldbook.iupac.org/terms/view/F02520" target="_blank" title="free rotation (hindered rotation, restricted rotation) in Gold Book">hindered</a> biaryls [<a href="#Blue_Book_2014" title="Blue Book (2014)">1</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93050701" target="_blank" title="Blue Book, P-93.5.7.1">P-93.5.7.1</a>], which exhibit a type of isomerism know as <a href="http://en.wikipedia.org/wiki/Atropisomer" target="_blank" title="Atropisomer in Wikipedia"><i>atropisomerism</i></a>. The Gold Book defines <a href="http://goldbook.iupac.org/terms/view/A00511" target="_blank" title="atropisomers in Gold Book"><i>atropisomers</i></a> as “subclass of conformers which can be isolated as separate chemical species and which arise from restricted rotation about a single bond”. For instance, <b>(e)</b> and <b>(f)</b> are atropisomers of <a href="http://en.wikipedia.org/wiki/1,1%E2%80%B2-Bi-2-naphthol" target="_blank" title="1,1′-Bi-2-naphthol in Wikipedia">1,1′-bi-2-naphthol</a> that result from rotation about the single bond connecting the two 2-naphthol moieties. This bond lies on the chirality axis. The structure <b>(e)</b> is a mirror image of <b>(f)</b>, so the pair are <i>atropoenantiomers</i>. </p>
<center>
<table>
<tr><td><a href="http://commons.wikimedia.org/wiki/File:(S)-BINOL.svg" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="File:(S)-BINOL.svg @ Wikimedia"><img border="0" height="200" src="https://upload.wikimedia.org/wikipedia/commons/d/df/%28S%29-BINOL.svg" width="200" /></a></td>
<td><a href="http://commons.wikimedia.org/wiki/File:(R)-BINOL.svg" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="File:(R)-BINOL.svg @ Wikimedia"><img border="0" height="200" src="https://upload.wikimedia.org/wikipedia/commons/d/d1/%28R%29-BINOL.svg" width="200" /></a></td></tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> (1<i>P</i>)-[1,1′-binaphthalene]-2,2′-diol (<i>ring assembly + substitutive; PIN</i>) <br />
(1<i>S</i><sub>a</sub>)-[1,1′-binaphthalene]-2,2′-diol (<i>ring assembly + substitutive</i>) </li>
<li> (1<i>M</i>)-[1,1′-binaphthalene]-2,2′-diol (<i>ring assembly + substitutive; PIN</i>) <br />
(1<i>R</i><sub>a</sub>)-[1,1′-binaphthalene]-2,2′-diol (<i>ring assembly + substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> Applying the CIP sequence rules, we assign the priorities to the <a href="http://en.wikipedia.org/wiki/Naphthalene" target="_blank" title="Naphthalene in Wikipedia">naphthalene</a> ring atoms directly connected to the atoms C-1 and C-1′ of 1,1′-bi-2-naphthol. Since oxygen is senior to carbon, C(O,C,C) > C(C,C,C), so C-2 has priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> and C-8a has priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②</span>. Once again, we have two axes, <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①–②</span> and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′–②′</span>, perpendicular to the chirality axis and to each other. Employing the methods <a href="#PM_convention" title="P/M convention and Ra/Sa convention">described above</a>, we can name the structure <b>(e)</b> (1<i>P</i>)-[1,1′-binaphthalene]-2,2′-diol (PIN) or (1<i>S</i><sub>a</sub>)-[1,1′-binaphthalene]-2,2′-diol, and its enantiomer <b>(f)</b> (1<i>M</i>)-[1,1′-binaphthalene]-2,2′-diol (PIN) or (1<i>R</i><sub>a</sub>)-[1,1′-binaphthalene]-2,2′-diol. </p>
<p> In axially chiral biaryl natural products there is marked preference of one atropisomer over the other. For example, the antibacterial and cytotoxic compound <a href="http://en.wikipedia.org/wiki/Viriditoxin" target="_blank" title="Viriditoxin in Wikipedia">viriditoxin</a> was isolated from several species of fungi, mostly as (<i>M</i>) atropisomer <b>(g)</b>, with trace amounts of (<i>P</i>) atropisomer <b>(h)</b> [<a href="#Hu_2019" title="Hu et al.(2019)">4</a>]. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:146007" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(M)-viriditoxin (CHEBI:146007)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgw-3AugC450Pkf3oHcNwqJFs-tJHFenwIRFFvmVZ2r7EfKTKbozYwb3ACxcCwxBi0L72TFVSQxnLLk8e566Wh6lvrTwcWJY7PIVqv6OW7glF982GAEG411WDB3L6rCPayP5OVqTvJMbZlXT8yTri-RYlLUqy3bmQv-YMyDB6u85hQcDI_IybWRpA/w200-h200/M-viriditoxin.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:146016" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(P)-viriditoxin (CHEBI:146016)"><img alt="" border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh8GRsO2TJ3iRRS40ZJ1l1Kj67eCDkFV3Lm1E12t8lNEFQYTgJzz-gBfTbyAJBal14oSWs5y4OTHFnYSX9sdoma-zv4Fuw7AC2ry92HEQOIOW7hsF9AonHavh7KGIxBWE_4VHiA8PLx-IBgnzS2p4Fx9lo6a_Fd7NlVDnTixPsWA9ihP1_tYSSSbw/w200-h200/P-viriditoxin.png" width="200" /></a></td>
</tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> (<i>M</i>)-viriditoxin (<i>trivial</i>) <br />
dimethyl 2,2′-[(3<i>S</i>,3′<i>S</i>,6<i>M</i>)-9,9′,10,10′-tetrahydroxy-7,7′-dimethoxy-1,1′-dioxo-3,3′,4,4′-tetrahydro-1<i>H</i>,1′<i>H</i>-[6,6′-binaphtho[2,3-<i>c</i>]pyran]-3,3′-diyl]diacetate (<i>ring assembly + substitutive</i>) </li>
<li> (<i>P</i>)-viriditoxin (<i>trivial</i>) <br />
dimethyl 2,2′-[(3<i>S</i>,3′<i>S</i>,6<i>P</i>)-9,9′,10,10′-tetrahydroxy-7,7′-dimethoxy-1,1′-dioxo-3,3′,4,4′-tetrahydro-1<i>H</i>,1′<i>H</i>-[6,6′-binaphtho[2,3-<i>c</i>]pyran]-3,3′-diyl]diacetate (<i>ring assembly + substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> Note that in addition to the chirality axis (collinear with the C-6—C-6′ bond), viriditoxin has two chiral atoms (C-3 and C-3′). The structures <b>(g)</b> and <b>(h)</b> are not enantiomers but <i>atropodiastereomers</i>. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> It is not clear how the descriptors ‘<i>R</i><sub>a</sub>’ and ‘<i>S</i><sub>a</sub>’ are supposed to be <i>pronounced</i>. “<i>R</i> axial” and “<i>S</i> axial” sound more Spanish than English because the adjective “axial” follows the descriptor. On the other hand, I saw the descriptors ‘<sub>a</sub><i>R</i>’ and ‘<sub>a</sub><i>S</i>’ used in Spanish chemical literature [<a href="#Quiroga_Feijoo_2007" title="Quiroga Feijóo (1968)">2</a>, p. 125]. Do the Spanish speakers pronounce them English way, that is, “axial <i>R</i>” and “axial <i>S</i>”? Go figure. (Cf. <a href="http://metallome.blogspot.com/2024/02/planar-chirality.html" target="_blank" title="Planar chirality @ this blog">planar chirality</a> descriptors ‘<i>R</i><sub>p</sub>’ and ‘<i>S</i><sub>p</sub>’.) </td></tr>
<tr><td valign="top">†</td>
<td> So called because it was first isolated from the grasshopper, <a href="http://species.wikimedia.org/wiki/Romalea_microptera" target="_blank" title="Romalea microptera in Wikispecies"><i>Romalea microptera</i></a> [<a href="#Meinwald_1968" title="Meinwald et al. (1968)">3</a>] but later found in other organisms such as algae and higher plants. </td></tr>
</table>
<h4>References</h4>
<ol>
<a name="Blue_Book_2014"></a>
<li>Favre, H.A. and Powell, W.H. <a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
<a name="Quiroga_Feijoo_2007"></a>
<li> Quiroga Feijóo, M.L. <a href="https://amzn.to/3SaZccP" target="_blank" title="Estereoquímica @ Amazon.co.uk"><i>Estereoquímica: conceptos y aplicaciones en química orgánica</i></a>. Editorial Síntesis, Madrid, 2007. </li>
<a name="Meinwald_1968"></a>
<li> Meinwald, J., Erickson, K., Hartshorn, M., Meinwald, Y.C. and Eisner, T. (1968) Defensive mechanisms of arthropods. XXIII. An allenic sesquiterpenoid from the grasshopper <i>Romalea microptera</i>.
<a href="http://doi.org/10.1016/S0040-4039(00)89622-7" target="_blank" title="Meinwald et al. (1968) Tetrahedron Lett. 9, 2959-2962."><i>Tetrahedron Letters</i> <b>9</b>, 2959—2962</a>. </li>
<a name="Hu_2019"></a>
<li> Hu, J., Li, H. and Chooi, Y.-H. (2019) Fungal dirigent protein controls the stereoselectivity of multicopper oxidase-catalyzed phenol coupling in viriditoxin biosynthesis. <a href="http://doi.org/10.1021/jacs.9b03354" target="_blank" title="Hu et al. (2019) J. Am. Chem. Soc. 141, 8068-8072."><i>Journal of the American Chemical Society</i> <b>141</b>, 8068—8072</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-55924771245173754492023-09-27T23:00:00.020+01:002023-12-09T00:08:32.439+00:00cis and trans<p> What’s the difference between the structures <b>(a)</b> and <b>(b)</b>? </p>
<center>
<table>
<tbody><tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:48366" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cis-but-2-ene (CHEBI:48366)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjssHTWyW8nQvNDLPgi2q8M_JT5r67kWh97f-k9uQlNiwgkHjmvmMB4LGCTx-lDvw2gA1Kw6yGyMsV_3h-sODdxDHgbGtwoIqZxaSSsxMQwvpim3HPTWhFe9AITiZUOShxok3BC_iZnu8ZHs-91FjKYHWecTbEMfGJZx9LjlgmOOxWHgKswqpcvVg/s1600/cis-but-2-ene.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:48365" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="trans-but-2-ene (CHEBI:48365)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjA9vJi6GPpZ2dNilBvkuW--tLT27KoZWp2sN21-fdUFH8WKDqPsKhWws2rva27obU2XadfUdzG7i_V_GF6R5shkjIDRktCUFbSY3uwCvsmqqOS0E7P6GmNgnkZ0oZdG56IJ62EGVmP54kQBBBh7IKioTFOZjoxeXnmBc-N98SQ__1rwxpQKrjlnA/s1600/trans-but-2-ene.png" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th>
</tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="1" type="a">
<li> (2<i>Z</i>)-but-2-ene (<i>PIN</i>) <br />
<i>cis</i>-but-2-ene </li>
<li> (2<i>E</i>)-but-2-ene (<i>PIN</i>) <br />
<i>trans</i>-but-2-ene </li>
</ol>
</td></tr>
</tbody></table>
</center>
<a name='more'></a>
<p> Why, isn’t it obvious: in the former structure, the two methyl groups are found on the same side of the double bond while in the latter they are on the opposing sides<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. Both compounds can be named <a href="http://en.wikipedia.org/wiki/But-2-ene" target="_blank" title="But-2-ene in Wikipedia">but-2-ene</a>. However, to distinguish between <b>(a)</b> and <b>(b)</b>, they are decribed respectively as <i>cis</i>-but-2-ene and <i>trans</i>-but-2-ene. The corresponding stereodescriptors are derived from the Latin prepositions <a href="http://en.wiktionary.org/wiki/cis#Latin" target="_blank" title="cis in Wiktionary"><i>cis</i></a>, “(on) this side of”, and <a href="http://en.wiktionary.org/wiki/trans#Latin" target="_blank" title="trāns in Wiktionary"><i>trāns</i></a>, “across”. Perhaps unsurprisingly, such molecules are called <a href="http://goldbook.iupac.org/terms/view/C01093" target="_blank" title="cis-trans isomers in Gold Book"><i>cis-trans isomers</i></a>. The earlier term <a href="http://goldbook.iupac.org/terms/view/G02620" target="_blank" title="geometric isomerism [obsolete] in Gold Book"><i>geometric isomers</i></a> is “strongly discouraged” by IUPAC [<a href="#Moss_1996" title="Moss (1996)">2</a>] but remains in wide use. </p>
<p> We have already seen an example of <i>cis-trans</i> isomerism when looking at <a href="http://metallome.blogspot.com/2023/08/polyhedral-symbols-configuration-indices.html#cis-trans" target="_blank" title="Polyhedral symbols and configuration indices @ this blog">diamminedichloridoplatinum(<small>II</small>)</a>. In coordination chemistry, <i>cis-trans</i> isomers are usually found in square planar (<i>SP</i>-4) complexes of the form [Ma<sub>2</sub>b<sub>2</sub>]. Similarly, organic <i>cis-trans</i> isomers such as <b>(a)</b> and <b>(b)</b> show tetragonal planar geometry of the form [abC=Cab]. </p>
<p> What if we substitute one of the hydrogens at the double bond in but-2-ene with another group? Then we’ll have a structure of the form [abC=Cbc] and a different system to describe its configuration will be needed. </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36431" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="angelic acid (CHEBI:36431)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7HvHNGXKJ1zuty6WKaFYkFfV4SyiDBt0KboocddeAZKZ9HMk1r1UfnOn7F3bUN5Vq-j858AqlPfSpA-xVfILKBgIVL9sjVWpVeTK9OusGdlYbj6A1vWAnrzbSwf4df98pPwQrOMMHqIk_3NRZ-Phf-hPt4vU7Pjvf-P5ReJG0H_f0c0XMDVUS3g/s16000/angelic_acid.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:9592" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tiglic acid (CHEBI:9592)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBDDCiRlW5aFZzd9fcniTtSwJGQYAN3ulZoxQEJrbZzxeXLps_fWREzIOvW8ub9XYBEAZspqG4IKJK60cC8Gnp0FtZ8g6WUxbrXwkxLJ8-bbv4h7U06z-weY_rEeHFBaRozsFpU-MwNZ4PjE8nAGReYVEVO7lZiht3mJNAgikVOP-J6lcDUtKYlw/s1600/tiglic_acid.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="3" type="a">
<li> angelic acid (<i>trivial</i>) <br />
(2<i>Z</i>)-2-methylbut-2-enoic acid (<i>substitutive</i>) </li>
<li> tiglic acid (<i>trivial</i>) <br />
(2<i>E</i>)-2-methylbut-2-enoic acid (<i>substitutive</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> The system recommended by IUPAC is the <i>E</i>/<i>Z</i> convention [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9102010201" target="_blank" title="Blue Book, P-91.2.1.2.1">P-91.2.1.2.1</a>]. To take a well-deserved break from Greek and Latin, the descriptors ‘<i>E</i>’ and ‘<i>Z</i>’ are derived from the German words <a href="http://en.wiktionary.org/wiki/entgegen" target="_blank" title="entgegen in Wiktionary"><i>entgegen</i></a>, “against” and <a href="http://en.wiktionary.org/wiki/zusammen" target="_blank" title="zusammen in Wiktionary"><i>zusammen</i></a>, “together”. Like the <a href="http://metallome.blogspot.com/2023/09/enantiomers.html#RS" target="_blank" title="Enantiomers: R/S @ this blog"><i>R</i>/<i>S</i></a> and <a href="http://metallome.blogspot.com/2023/09/enantiomers.html#CA" target="_blank" title="Enantiomers: C/A @ this blog"><i>C</i>/<i>A</i></a> conventions, the <i>E</i>/<i>Z</i> convention makes use of <a href="http://en.wikipedia.org/wiki/Cahn%E2%80%93Ingold%E2%80%93Prelog_priority_rules" target="_blank" title="Cahn–Ingold–Prelog priority rules in Wikipedia">Cahn–Ingold–Prelog</a> (CIP) sequence rules to assign the priorities to the atoms or groups. </p>
<p> Let’s see how it works on the example of the charmingly named <a href="http://en.wikipedia.org/wiki/Angelic_acid" target="_blank" title="Angelic acid in Wikipedia">angelic acid</a> <b>(c)</b><sup><a href="#Footnote_†" title="Footnote †">†</a></sup>. Its structure looks like that of <i>trans</i>-but-2-ene <b>(b)</b> substituted with carboxy group. Carboxy group is senior to methyl; on the other end of the double bond, we have methyl group that is senior to hydrogen. So, the higher-priority group at C-2 (carboxy) is <i>cis</i> to the higher-priority group at C-3 (methyl) and the full systematic name of <b>(c)</b> is (2<i>Z</i>)-2-<span style="background-color: lavender;">methyl</span><span style="background-color: yellow;">but-2-en</span><span style="background-color: lavender;">oic acid</span>. On the contrary, tiglic acid <b>(d)</b> will be named (2<i>E</i>)-2-<span style="background-color: lavender;">methyl</span><span style="background-color: yellow;">but-2-en</span><span style="background-color: lavender;">oic acid</span>. </p>
<p> We can employ the <i>E</i>/<i>Z</i> convention even when the <i>cis</i>/<i>trans</i> notation is perfectly adequate. In fact, the <i>E</i>/<i>Z</i> names are preferred by IUPAC: (2<i>Z</i>)-but-2-ene <b>(a)</b> and (2<i>E</i>)-but-2-ene <b>(b)</b>. </p>
<p> The descriptors ‘<i>E</i>’ and ‘<i>Z</i>’ can also be used with non-carbon double bonds [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9304020103" target="_blank" title="Blue Book, P-93.4.2.1.3">P-93.4.2.1.3</a>]. </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:58997" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(Z)-azobenzene (CHEBI:58997)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAzxfuQkqQ7i3ZE7AMLNgydWlGRDJvDfHN8GwlBoXM6X44ol-S0wGKolS7wq7AU2b0e_FggMYfizHVMLewauw3YgH1-E_S23_o0BeStNZH145xWojZoVxymzEdViXirsABHH1v4nZh4lmSaKMmkPdU4hxUL-cdkxoSix6cOYgwOaGU_5ZYS-JrSA/s1600/cis-azobenzene.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51868" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cis-azoxybenzene (CHEBI:51868)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQ6BpYdDxbWbz0ByQ6zXW2YBOo-kxk77zJpAQIZQ4jaRXh0t_vo5kD5Jc3lSywboXTEXlocNTtCngQn-fqnrQXYjU2bj2gW9A5kBNwMuAwOag0CcOMCDcF2nJlsyFLiAKlIsbPxN_YI8FuqWvg-RkWxKhi5zC_CR6lqaOpD6Su1ioundof1rpp-A/s1600/cis-azoxybenzene.png" width="200" /></a></td></tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="5" type="a">
<li> <i>cis</i>-azobenzene (<i>trivial</i>) <br />
(<i>Z</i>)-diphenyldiazene (<i>substitutive, PIN</i>) </li>
<li> <i>cis</i>-azoxybenzene (<i>trivial</i>) <br />
(<i>E</i>)-diphenyldiazene oxide (<i>substitutive + additive, PIN</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> Have a look at <i>cis</i>-azobenzene <b>(e)</b> and its derivative, <i>cis</i>-azoxybenzene <b>(f)</b>. The lone pair of electrons is considered to have zero atomic number. The higher-priority groups (phenyls) in <b>(e)</b> are <i>cis</i> (<i>zusammen</i>!) to each other and so the systematic name is (<i>Z</i>)-<span style="background-color: lavender;">diphenyl</span><span style="background-color: yellow;">diazene</span>. Now applying the CIP rules to <b>(f)</b>, we’ll see that the higher-priority group at the first nitrogen atom is oxo (O > C) which is <i>trans</i> (<i>entgegen</i>!) to the higher-priority group at the second nitrogen, viz. phenyl (C > lone pair). Therefore, the systematic name of <b>(f)</b> will be (<i>E</i>)-<span style="background-color: lavender;">diphenyl</span><span style="background-color: yellow;">diazene</span> <span style="background-color: lightgreen;">oxide</span>. IUPAC does not recommend ‘<i>cis</i>’ and ‘<i>trans</i>’ for double bonds linked to heteroatoms [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9304020103" target="_blank" title="Blue Book, P-93.4.2.1.3">P-93.4.2.1.3</a>]. </p>
<p> Another type of <i>cis-trans</i> isomerism is found in ring systems [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93050102" target="_blank" title="Blue Book, P-93.5.1.2">P-93.5.1.2</a>]. Observe the isomers of 1,4-<span style="background-color: lavender;">dimethyl</span><span style="background-color: yellow;">cyclohexane</span>: </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:167602" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cis-1,4-dimethylcyclohexane (CHEBI:167602)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwPxU-tjdY0_LexyOyAH0nLUAxSYWB7l64xJHeARpiraPUaYMK4lZ21iw0vlEx56jHQMJgF97-Y_v56nsm_rfpUiAHle7JRSNQStkh1PzwgIVv0gWHpj1NMy-pcYzzlif106HTzNubrQw7VrXkik9Zyh0-tkOWi28mPPuuiBymvjvl3VkSd9GJgg/s1600/cis-1,4-dimethylcyclohexane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:167603" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="trans-1,4-dimethylcyclohexane (CHEBI:167603)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjCYpx-0Q_UcPgFmPx3JipH0cXqyaWJHU_7RCzqQ6aSVja3ENYAwH6AYjpR7knM11UE-D0S-7sNVHzVhxeGNZfdDW2wRJ-PDMtVJ6hxaYd-vLhbsY30AP53tMweTa1fpR-f7vS4LfzkfoStON3jAmA64FLpW12xc_fB-bKhcuBgmi8yDtfyX3w3VA/s1600/trans-1,4-dimethylcyclohexane.png" width="200" /></a></td></tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="7" type="a">
<li> <i>cis</i>-1,4-dimethylcyclohexane (<i>substitutive</i>) </li>
<li> <i>trans</i>-1,4-dimethylcyclohexane (<i>substitutive</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> In the structure <b>(g)</b>, the two methyl groups are on the same side of the plane of a ring<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>, so this isomer is called <i>cis</i>-1,4-<span style="background-color: lavender;">dimethyl</span><span style="background-color: yellow;">cyclohexane</span>. In <b>(h)</b>, the methyls are on opposite sides of the plane, thus <i>trans</i>-1,4-<span style="background-color: lavender;">dimethyl</span><span style="background-color: yellow;">cyclohexane</span>. </p>
<p> As in case of the double bond, there is no <a href="http://goldbook.iupac.org/terms/view/F02520" target="_blank" title="free rotation (hindered rotation, restricted rotation) in Gold Book">free rotation</a> between the atoms in the ring. However, the saturated carbon atoms in the rings have tetrahedral geometry, as opposed to trigonal planar one in alkenes. Which could mean... more stereoisomers! </p>
<center>
<table>
<tbody><tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16190" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cis-cyclohexa-3,5-diene-1,2-diol (CHEBI:16190)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcVpWsXyuKLpxovpS0k4MKxTrJpIWtMb4m5AwIsoe5kAOdiuRhUgNZvTNvvgZa2k17O-irT5VuLnJt7CrB91toiyG8JwSRekEBlph_qs5wNB93jDAtcrgcGKsl6l2dSXi8ax9BNAFrbNMR8piB9iehmHk7xIdqkeu3rcjbifdMiRw7mjgEo6chzg/s1600/cis-cyclohexa-3,5-diene-1,2-diol.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:10702" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(1R,2R)-cyclohexa-3,5-diene-1,2-diol (CHEBI:10702)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5cQzFix1PQm3zzgnTScDShNSL0nkPf4KS5-QV_C5reLgu90SgGL2dK-KysJnV3Tum2vfmzfa59wgr5p9SweDHkS9qz03q3CASGiuwrqExHbbf8k9G_IEXV2tpD0KgsaZHU3CvjZzE4gxErzVZwLtl-DtiwZwWZ4srcRJgtrN22P8EVK9So0DT_Q/s1600/(1R,2R)-cyclohexa-3,5-diene-1,2-diol.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:12855" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(1S,2S)-cyclohexa-3,5-diene-1,2-diol (CHEBI:12855)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicEafEwfwqUNJ-Oa8DDArURN_BJp4EWAOfogNgokv9zPrClJcmlIJdzGf1zjrQY-0XMvpabbL8g75DhTN_WFSn7myi6L4Px-l9MxwZ_B3TAf3JPDTv71GCELxJTr5WFAKkeiA7s3DGSD3mCS4PFnOk5ZtwuoEd6bMJT5odRPOYMZcAQOQGu7xWzg/s1600/(1S,2S)-cyclohexa-3,5-diene-1,2-diol.png" width="200" /></a></td></tr>
<tr><th align="center">(i)</th> <th align="center">(j)</th> <th align="center">(k)</th>
</tr>
</tbody></table>
</center>
<center>
<table>
<tbody><tr>
<td><ol start="9" type="a">
<li> <i>cis</i>-cyclohexa-3,5-diene-1,2-diol (<i>substitutive</i>) <br />
(1<i>R</i>,2<i>S</i>)-cyclohexa-3,5-diene-1,2-diol (<i>substitutive</i>) </li>
<li> (1<i>R</i>,2<i>R</i>)-cyclohexa-3,5-diene-1,2-diol (<i>substitutive</i>) </li>
<li> (1<i>S</i>,2<i>S</i>)-cyclohexa-3,5-diene-1,2-diol (<i>substitutive</i>) </li>
</ol>
</td></tr>
</tbody></table>
</center>
<p> There are three possible stereoisomers of <span style="background-color: yellow;">cyclohexa-3,5-diene</span>-1,2-<span style="background-color: lavender;">diol</span>: one <i>cis</i> <b>(i)</b> and two <i>trans</i>, <b>(j)</b> and <b>(k)</b>, the latter pair being enantiomers. For them just ‘<i>trans</i>’ is not a good enough descriptor: we need the <i>R</i>/<i>S</i> convention. If we don’t know which of the two <i>trans</i> isomers we are talking about, we can employ the descriptor ‘<i>rel</i>’ that indicates the relative configuration of one chiral centre with respect to (any) other chiral centre [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93010201" target="_blank" title="Blue Book, P-93.1.2.1">P-93.1.2.1</a>]. So <i>rel</i>-(1<i>R</i>,2<i>R</i>)-<span style="background-color: yellow;">cyclohexa-3,5-diene</span>-1,2-<span style="background-color: lavender;">diol</span> means “(1<i>R</i>,2<i>R</i>)-<span style="background-color: yellow;">cyclohexa-3,5-diene</span>-1,2-<span style="background-color: lavender;">diol</span> <i>or</i> its enantiomer”. We also can describe <b>(i)</b> as (1<i>R</i>,2<i>S</i>)-<span style="background-color: yellow;">cyclohexa-3,5-diene</span>-1,2-<span style="background-color: lavender;">diol</span>, but why should we do that if <i>cis</i>-<span style="background-color: yellow;">cyclohexa-3,5-diene</span>-1,2-<span style="background-color: lavender;">diol</span> is shorter and as unambiguous? </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tbody><tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> If it’s not intuitively clear what the “same side” or “opposite side” of a bond mean, we can use the concept of “a reference plane identifiable as common among stereoisomers”. For double bonds, “the reference plane contains the doubly bonded atoms and is perpendicular to the plane containing these atoms and those directly attached to them” [<a href="#Cross_and_Klyne_1976" title="Cross & Klyne (1976)">1</a>, E-2.1]. For example, the reference plane is perpendicular to the plane of the diagrams <b>(a)</b>—<b>(f)</b>. </td></tr>
<tr><td valign="top">†</td>
<td> Angelic acid is called so because it was first isolated from the roots of angelica (<a href="http://en.wikipedia.org/wiki/Angelica_archangelica" target="_blank" title="Angelica archangelica in Wikipedia"><i>Angelica archangelica</i></a>). Its salts and esters are known as angelates. </td></tr>
<tr><td valign="top">‡</td>
<td> Here, “the reference plane is that in which the ring skeleton lies or to which it approximates” [<a href="#Cross_and_Klyne_1976" title="Cross & Klyne (1976)">1</a>, E-2.1]. </td>
</tr>
</tbody></table>
<h4>References</h4>
<ol>
<a name="Cross_and_Klyne_1976"></a>
<li> Cross, L.C. and Klyne, W. (1976) Nomenclature of Organic Chemistry. Section E: Stereochemistry (Recommendations 1974). <a href="http://publications.iupac.org/pac/1976/pdf/4501x0011.pdf" target="_blank" title="Pure Appl. Chem. 45, 11-30."><i>Pure and Applied Chemistry</i> <b>45</b>, 11—30</a>. </li>
<a name="Moss_1996"></a>
<li> Moss, G.P. (1996) Basic terminology of stereochemistry (IUPAC Recommendations 1996). <a href="http://doi.org/10.1351/pac199668122193" target="_blank" title="Moss (1996) Pure Appl. Chem. 68, 2193-2222."><i>Pure and Applied Chemistry</i> <b>68</b>, 2193—2222</a>.
<a name="Blue_Book_2014"></a>
</li><li>Favre, H.A. and Powell, W.H. <a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-16789613365572538352023-09-13T23:00:00.023+01:002024-03-16T13:29:02.204+00:00Enantiomers<link href="http://fonts.googleapis.com/css?family=Noto+Sans+Symbols" rel="stylesheet" type="text/css">
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<p> Have a look at the structures <b>(a)</b> and <b>(b)</b>. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:4469" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(S)-amphetamine (CHEBI:4469)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_WmApwX7KARkxlGUc_YWm7BOzLlYpoLz1sictAZZMqX-jZRYm62EHCWJsz-vFXGTo7QNWEv8yloZhXfVgaJUFCK2Al9wT4LyRp9pExYT-DyDDKrE3B0CQU026p8krzPDOUPmZ_85cU1_k4-y8cD_WkGJTcRFSDUI5Xzwrvu6fBfYXzqPnfL-5fQ/s1600/S-amphetamine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:42724" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(R)-amphetamine (CHEBI:42724)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNt1IRmwphH8-Xyakw58u3xR2fckAzFtgtzlcQc7w_75hTdHPGzFZ6jB5Mv-Hp8WoHdnBbpHI-9iiwGPpti1M-w8Ef3AkW9k2AfowX1xRYIDurUABPxZFQ2kEl0yYotU11hlG4dmxjY-AIZhjLiKTOc1jZLA-S0XnpRJmiyMTgDvctyjNteL7txw/s1600/R-amphetamine.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> (+)-amphetamine (<i>trivial</i>) <br />
<i>d</i>-amphetamine (<i>trivial</i>) <br />
dextroamphetamine (<i>trivial</i>) <br />
dexamfetamine (<i>INN</i>) <br />
(2<i>S</i>)-1-phenylpropan-2-amine (<i>substitutive</i>) </li>
<li> (−)-amphetamine (<i>trivial</i>) <br />
<i>l</i>-amphetamine (<i>trivial</i>) <br />
levoamphetamine (<i>trivial</i>) <br />
levamfetamine (<i>INN</i>) <br />
(2<i>R</i>)-1-phenylpropan-2-amine (<i>substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<a name='more'></a>
<p> They could be thought of as mirror images of each other: one structure cannot be superposed on the other. Such molecules are known as <a href="http://goldbook.iupac.org/terms/view/E02069" target="_blank" title="enantiomer in Gold Book"><i>enantiomers</i></a>. </p>
<a name="(+)(−)"></a>
<h3><small>(+)/(−)</small></h3>
<p> A pair of enantiomers often could be distinguished by their contrary <a href="http://en.wikipedia.org/wiki/Optical_rotation" target="_blank" title="Optical rotation in Wikipedia">optical activity</a>, that is, rotation of plane-polarised light in opposite directions. Our <b>(a)</b> and <b>(b)</b> are two enantiomers of <a href="http://en.wikipedia.org/wiki/Amphetamine" target="_blank" title="Amphetamine in Wikipedia">amphetamine</a>: <a href="http://en.wikipedia.org/wiki/Dextroamphetamine" target="_blank" title="Dextroamphetamine in Wikipedia">dextroamphetamine</a> [also known as dexamfetamine, <i>d</i>-amphetamine, and (+)-amphetamine] and <a href="http://en.wikipedia.org/wiki/Levoamphetamine" target="_blank" title="Levoamphetamine in Wikipedia">levoamphetamine</a> [levamfetamine, <i>l</i>-amphetamine, (−)-amphetamine], respectively. In these names, ‘<a href="http://en.wiktionary.org/wiki/dextro-" target="_blank" title="dextro- in Wiktionary">dextro</a>’, ‘<a href="http://en.wiktionary.org/wiki/dex-" target="_blank" title="dex- in Wiktionary">dex</a>’, ‘<i>d</i>’ (all from the Latin word <a href="http://en.wiktionary.org/wiki/dexter#Latin" target="_blank" title="dexter in Wiktionary"><i>dexter</i></a>, “right”) and ‘(+)’ refer to <i>dextrorotation</i>, i.e. right-hand or clockwise optical rotation, by this substance; and ‘<a href="http://en.wiktionary.org/wiki/levo-" target="_blank" title="levo- in Wiktionary">levo</a>’, ‘<a href="http://en.wiktionary.org/wiki/lev-" target="_blank" title="lev- in Wiktionary">lev</a>’, ‘<i>l</i>’ (from the Latin <a href="http://en.wiktionary.org/wiki/laevus#Latin" target="_blank" title="laevus in Wiktionary"><i>laevus</i></a>, “left”) and ‘(−)’ indicate <i>levorotation</i>, i.e. left-hand or anticlockwise (counterclockwise) rotation<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. The historical descriptors <i>d</i> and <i>l</i> could be easily confused with descriptors <small>D</small> and <small>L</small>; the former are deprecated by IUPAC [<a href="#Cross_and_Klyne_1976" title="Cross & Klyne (1976)">1</a>]. </p>
<p> A mixture containing equal amounts of a pair of enantiomers is called <a href="http://goldbook.iupac.org/terms/view/R05025" target="_blank" title="racemate in Gold Book"><i>racemate</i></a>. Such mixtures could be named using descriptors ‘<i>rac</i>’ or ‘(±)’; for example, an equimolar mixture of <b>(a)</b> and <b>(b)</b> is known as <i>rac</i>-amphetamine or (±)-amphetamine. </p>
<p> Descriptors such as ‘<i>rac</i>’ or ‘(±)’ refer to a physical property (absence of optical activity) observed in a macroscopic system, which could be a solution or a crystal but not a single molecule. Likewise, descriptors ‘(+)’, ‘(−)’, ‘<i>d</i>’, ‘<i>l</i>’, tell us that the system <i>has</i> optical activity. The system does not have to be a pure enantiomer to show dextrorotation: it could be a mixture with an excess of the ‘(+)’ isomer over the ‘(−)’ one.
</p>
<a name="RS"></a>
<h3><small><i>R</i>/<i>S</i></small></h3>
<p> Now let’s give systematic names to our structures. Amphetamine can be named substitutively 1-<span style="background-color: lavender;">phenyl</span><span style="background-color: yellow;">propan</span>-2-<span style="background-color: lavender;">amine</span>. The structural difference between <b>(a)</b> and <b>(b)</b> lies in a spatial arrangement, or <a href="http://goldbook.iupac.org/terms/view/A00020" target="_blank" title="absolute configuration in Gold Book">absolute configuration</a>, of four different ligands, viz. hydrogen, amino group ‒NH<sub>2</sub>, benzyl group ‒CH<sub>2</sub>‒C<sub>6</sub>H<sub>5</sub>, and methyl ‒CH<sub>3</sub>, attached to the chiral carbon atom (C-2). To determine the configuration, the ligands are assigned priorities based on <a href="http://en.wikipedia.org/wiki/Cahn%E2%80%93Ingold%E2%80%93Prelog_priority_rules" target="_blank" title="Cahn–Ingold–Prelog priority rules in Wikipedia">Cahn–Ingold–Prelog</a> (CIP) sequence rules. </p>
<p> First, the atoms directly attached to the chiral centre are arranged in order of decreasing atomic number. In the structure <b>(a)</b>, the order of preference is N > C = C > H. Next, as there are two carbon atoms bound to the chiral centre, we have to look at the precedence of atoms directly attached to them [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9202010102" target="_blank" title="Blue Book, P-92.2.1.1.2">P-92.2.1.1.2</a>]. There are three hydrogen atoms in the methyl group: C(H,H,H), while the methylene carbon of the benzyl group is linked to two hydrogens and one carbon of the benzene ring: C(C,H,H). Since carbon is senior to hydrogen, C(C,H,H) > C(H,H,H), therefore, benzyl is senior to methyl. On the diagram <b>(a)</b>, the chiral centre is positioned in such a way that the least-preferred ligand — in this case, hydrogen — points <i>away</i> from the viewer; the rest of the ligand sequence, N > C<sub>benzyl</sub> > C<sub>methyl</sub>, go anticlockwise. This configuration is indicated with the stereodescriptor ‘<i>S</i>’ (from the Latin <a href="http://en.wiktionary.org/wiki/sinister#Latin" target="_blank" title="sinister in Wiktionary"><i>sinister</i></a>, “left”). This stereodescriptor is placed after the locant corresponding to the chiral atom, in our case, ‘2’, and enclosed in parentheses. Hence, the complete name of <b>(a)</b> will be (2<i>S</i>)-1-<span style="background-color: lavender;">phenyl</span><span style="background-color: yellow;">propan</span>-2-<span style="background-color: lavender;">amine</span>. In <b>(b)</b>, the ligands go in the opposite direction, i.e. clockwise, and the stereodescriptor ‘<i>R</i>’ (from the Latin <a href="http://en.wiktionary.org/wiki/rectus#Latin" target="_blank" title="rectus in Wiktionary"><i>rectus</i></a>, “right”<sup><a href="#Footnote_†" title="Footnote †">†</a></sup>), is used, thus (2<i>R</i>)-1-<span style="background-color: lavender;">phenyl</span><span style="background-color: yellow;">propan</span>-2-<span style="background-color: lavender;">amine</span>. </p>
<p> Although the <i>R</i>/<i>S</i> convention is most commonly used for chiral carbon atoms, it could be as easily applied to any other tetrahedral chiral centres, including metal atoms [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-9.3.4.2]. Moreover, the same symbols are employed to describe configuration of chiral trigonal pyramidal centres [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-9.3.4.3; <a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93030302" target="_blank" title="Blue Book, P-93.3.3.2">P-93.3.3.2</a>]. This is done by creating a tetrahedral centre by adding a “phantom atom” of the lowest priority to a trigonal pyramid. In compounds such as <a href="http://goldbook.iupac.org/terms/view/S06124" target="_blank" title="sulfoxides in Gold Book">sulfoxides</a> this phantom atom is placed in the site of a lone pair of electrons. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47809" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(S)-sulforaphane (CHEBI:47809)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj47r3fxeqoyx0MTydaCs7ukADHQuIJf6GBRXAhFE2dBuewz4UL1qPdZr5yG5uv6C9zy8HhQ1tzhpFeg3Tr2DtOREpWyiX6SZY7egwDpmcnvMmGrNCKeE5H20u2t0feSBoBXsluqponS2QZA9FeQJ0OmQMH8WYNqdiHVnOXa_tSTR3DjYE1skzD9w/s1600/S-sulforaphane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47808" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(R)-sulforaphane (CHEBI:47808)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6xnI2tVQd956sSkKytxTm9ypjVJ9RfLPicGEEznqtAvf10NpmHCr8GRyi_qjJju_Cldm-76as5meegmopqj_12y_bVgJlY_aYg4s-O4KhYhZE_mrijKyBBE9nwed_hxFC3DUMa80rGR1Zm6hhzYD3VRlKdhfuttusllskYpH2N0JoJtpudn5WRQ/s1600/R-sulforaphane.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> (<i>S</i>)-sulforaphane (<i>trivial</i>) <br />
1-isothiocyanato-4-[(<i>S</i>)-methanesulfinyl]butane (<i>substitutive</i>) <br />
4-isothiocyanatobutyl methyl (<i>S</i>)-sulfoxide (<i>functional class + substitutive</i>) </li>
<li> (<i>R</i>)-sulforaphane (<i>trivial</i>) <br />
1-isothiocyanato-4-[(<i>R</i>)-methanesulfinyl]butane (<i>substitutive</i>) <br />
4-isothiocyanatobutyl methyl (<i>R</i>)-sulfoxide (<i>functional class + substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> Consider <b>(c)</b> and <b>(d)</b>, the enantiomers of <a href="http://en.wikipedia.org/wiki/Sulforaphane" target="_blank" title="Sulforaphane in Wikipedia">sulforaphane</a>. Its purely substitutive name is 1-<span style="background-color: lavender;">isothiocyanato</span>-4-(<span style="background-color: lavender;">methanesulfinyl</span>)<span style="background-color: yellow;">butane</span>, but I prefer the shorter <a href="http://metallome.blogspot.com/2020/09/radicofunctional-names.html" target="_blank" title="Radicofunctional names @ this name">functional class</a> name, <span style="background-color: lightpink;">4-isothiocyanatobutyl</span> <span style="background-color: lightpink;">methyl</span> <span style="background-color: lightblue;">sulfoxide</span>. In the structure <b>(c)</b>, the seniority order of the ligands to the chiral sulfur atom is O > C = C. Since C(C,H,H) > C(H,H,H), 4-isothiocyanatobutyl group is senior to methyl. On the diagram <b>(c)</b>, the chiral centre is positioned so that the lone pair (or phantom atom) points <i>away</i> from the viewer; the sequence, O > C<sub>4-isothiocyanatobutyl</sub> > C<sub>methyl</sub>, go anticlockwise. Therefore, the complete name of <b>(c)</b> will be <span style="background-color: lightpink;">4-isothiocyanatobutyl</span> <span style="background-color: lightpink;">methyl</span> (<i>S</i>)-<span style="background-color: lightblue;">sulfoxide</span>, and that of its mirror image <b>(d)</b> <span style="background-color: lightpink;">4-isothiocyanatobutyl</span> <span style="background-color: lightpink;">methyl</span> (<i>R</i>)-<span style="background-color: lightblue;">sulfoxide</span>. </p>
<p> In contrast to macroscopic descriptors discussed above, ‘<i>R</i>’ and ‘<i>S</i>’ do not imply any optical activity or whatever other physical property: the “right” and “left” is just an arbitrary convention devised to distinguish between chiral centres. </p>
<a name="DL"></a>
<h3><small><span style="font-size: x-small;">D</span>/<span style="font-size: x-small;">L</span></small></h3>
<p> What if the molecule has more than one chiral centre? No problem, the <i>R</i>/<i>S</i> convention allows us to specify the absolute confuguration at every one of them. For instance, the structure <b>(e)</b> could be systematically named (2<i>R</i>,3<i>S</i>,4<i>R</i>,5<i>R</i>)-2,3,4,5,6-<span style="background-color: lavender;">pentahydroxy</span><span style="background-color: yellow;">hexan</span><span style="background-color: lavender;">al</span>. However, nobody will call it that because there is a much better name: <i>aldehydo</i>-<small>D</small>-glucose. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:42758" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="aldehydo-D-glucose (CHEBI:42758)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLEe7SNsQsrQGKsIXBlN4DFg7Hai75Rnt6vOVasGT4lgX01bdZpOsuUUocAOA9WrhMiBSySyr6GENk3pkjxbugt1DRpghDxQJZK6MeHWyLBQjV5m7k0u7bUuJbEp_q4lyHK5riVZdqHLJSFdKIfr8DkuVbyQMPQfXGwrffCNzOXSDUSOkBgt3Qag/s1600/aldehydo-D-glucose.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37626" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="aldehydo-L-glucose (CHEBI:37626)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEid8Iuk6deNhPZrvmB_g19oDTdh7bFWU6sfAdaf9k39H3DK5KRNVBLiYDE0tWf1o1VDx-viZnKcwJeNSc2EVK8H-sAjXD9HAB-Nu2Jm7YP3DoPznXtzginOm3GobKPjEvh5dqYjVUIJ5rScF2xVQBXVd1ylMD3Lc0glIFHE13zFl6q--KoNjjHLNg/s1600/aldehydo-L-glucose.png" width="200" /></a></td></tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> <i>aldehydo</i>-<small>D</small>-<i>gluco</i>-hexose (<i>carbohydrate</i>)<br />
<i>aldehydo</i>-<small>D</small>-glucose (<i>carbohydrate</i>)<br />
(2<i>R</i>,3<i>S</i>,4<i>R</i>,5<i>R</i>)-2,3,4,5,6-pentahydroxyhexanal (<i>substitutive</i>) </li>
<li> <i>aldehydo</i>-<small>L</small>-<i>gluco</i>-hexose (<i>carbohydrate</i>)<br />
<i>aldehydo</i>-<small>L</small>-glucose (<i>carbohydrate</i>)<br />
(2<i>S</i>,3<i>R</i>,4<i>S</i>,5<i>S</i>)-2,3,4,5,6-pentahydroxyhexanal (<i>substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> The stereodescriptor ‘<small>D</small>’ here has the same origin as the now obsolete ‘<i>d</i>’, i.e. <i>dexter</i>. One of the historical names of <a href="http://en.wikipedia.org/wiki/Glucose" target="_blank" title="Glucose in Wikipedia"><small>D</small>-glucose</a> is ‘dextrose’ because its aqueous solution shows dextrorotation. The use of modern stereodescriptors ‘<small>D</small>’ and ‘<small>L</small>’ in the names of sugars, however, does not depend on the optical rotation. To understand what’s going on, we have to look at the simplest monosaccharide that has a chiral centre: <a href="http://en.wikipedia.org/wiki/Glyceraldehyde" target="_blank" title="Glyceraldehyde in Wikipedia">glyceraldehyde</a>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17378" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="D-glyceraldehyde (CHEBI:17378)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-s2e2koLx__3jE1xAig2W6wDo9WyVq-lC2S5GGDS8GR-XyA5n3uIF3dZpGDNLkWVhSQGp1gNob2042Zj4_qeziKPnDHacSOWTZ7cVGZ7jb2OydrCivqR-f2q6oPPLqgvQrpT2542LTE1W_wNV48x05Ooae6zXpHSWJ-3Ar3xWiJsV-lUgRUoWBw/s1600/D-glyceraldehyde.png" width="200" /></a></td>
</tr>
<tr><th align="center">(g)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> <small>D</small>-glyceraldehyde (<i>carbohydrate</i>) <br />
<small>D</small>-<i>glycero</i>-triose (<i>carbohydrate</i>) <br />
(2<i>R</i>)-2,3-dihydroxypropanal (<i>substitutive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> The structure <b>(g)</b> is that of <small>D</small>-glyceraldehyde, which also could be named substitutively (2<i>R</i>)-2,3-<span style="background-color: lavender;">dihydroxy</span><span style="background-color: yellow;">propan</span><span style="background-color: lavender;">al</span>. In carbohydrate nomenclature, a monosaccharide is given either ‘<small>D</small>’ or ‘<small>L</small>’ descriptor according to the configuration of the chiral atom furthest from the carbonyl group, which is known as the <i>configurational atom</i> [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P10.html#1020303" target="_blank" title="Blue Book, P-102.3.3">P-102.3.3</a>]. In glucose, there are four chiral carbons: C-2, C-3, C-4 and C-5. We need to focus on C-5: if its configuration is the same as in <small>D</small>-glyceraldehyde — which is the case of the structure <b>(e)</b> — then the resulting name will also have ‘<small>D</small>’, as in <i>aldehydo</i>-<small>D</small>-glucose; otherwise, it is ‘<small>L</small>’. </p>
<p> What about the rest of the chiral atoms? Their <a href="http://goldbook.iupac.org/terms/view/R05260" target="_blank" title="relative configuration in Gold Book">relative configurations</a> are implicit in the ‘gluco’ bit. In the names like <i>aldehydo</i>-<small>D</small>-<i>gluco</i>-hexose, ‘gluco’ is referred to as a “configurational prefix” [<a href="#McNaught_1996" title="McNaught (1996)">4</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/2carb/03n04.html#043" target="_blank" title="Nomenclature of carbohydrates, 2-Carb-4.3. Configurational prefixes in systematic names">2-Carb-4.3</a>]. (We know by now that it is <a href="http://metallome.blogspot.com/2020/10/prefixes-or-combining-forms.html" target="_blank" title="Prefixes — or combining forms? @ this blog">not a prefix</a> but a combining form, that’s why I’ll keep the quotation marks). So instead of spelling out absolute configurations for <i>all</i> chiral centres using ‘<i>R</i>’ or ‘<i>S</i>’ descriptors, carbohydrate nomenclature specifies the absolute configuration of just one chiral centre (i.e. the configurational atom) using ‘<small>D</small>’ or ‘<small>L</small>’ while the relative configurations of other chiral centres are dealt with “configurational prefixes”. Resulting names are significantly shorter than substitutive ones; however, you need to look up what each “configurational prefix” means. </p>
<p> Apart from sugars, the stereodescriptors ‘<small>D</small>’ and ‘<small>L</small>’ are used in the nomenclature of cyclitols, amino acids and peptides [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9102010202" target="_blank" title="Blue Book, P-91.2.1.2.2">P-91.2.1.2.2</a>]. </p>
<a name="CA"></a>
<h3><small><i>C</i>/<i>A</i></small></h3>
<p> There is no reason why the <i>R</i>/<i>S</i> convention cannot be used for <a href="http://metallome.blogspot.com/2023/08/polyhedral-symbols-configuration-indices.html" target="_blank" title="Polyhedral symbols and configuration indices @ this blog">polyhedra</a> other than tetrahedron and trigonal pyramid. Indeed, the symbols ‘<i>R</i>’ and ‘<i>S</i>’ applied to octahedral systems are shown in earlier IUPAC recommendations [<a href="#Cross_and_Klyne_1976" title="Cross & Klyne (1976)">1</a>, p. 29, diagrams (17) and (18)]. However, for the “other” polyhedra it’s currently recommended to use the chirality symbols ‘<i>C</i>’ (from “clockwise”) and ‘<i>A</i>’ (“anticlockwise”) [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-9.3.4.4; <a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93030402" target="_blank" title="Blue Book, P-93.3.4.2">P-93.3.4.2</a>]. These symbols are cited following the polyhedral symbol and configuration index. </p>
<p> Let’s see how this works on the example of the octahedral complex <span style="background-color: lightgreen;">amminebromidochloridoiodidonitrito-κ<i>N</i>-(pyridine)</span><span style="background-color: gold;">platinum</span>(<small>IV</small>), or [PtBrClI(NH<sub>3</sub>)(NO<sub>2</sub>)(py)], which I shamelessly borrowed from the review of Constable [<a href="#Constable_2021" title="Constable (2021)">5</a>, <a href="http://www.mdpi.com/2073-8994/13/10/1891#symmetry-13-01891-f014" target="_blank" title="Constable (2021), Figure 14">Fig. 14</a>].
</p>
<center><img border="0" height="400" src="https://www.mdpi.com/symmetry/symmetry-13-01891/article_deploy/html/images/symmetry-13-01891-g014.png" width="374" /></center>
<p> In line with the CIP rules, the priorities of the ligands are: <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> (I), <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②</span> (Br), <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">③</span> (Cl), <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">④</span> (NO<sub>2</sub>), <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">⑤</span> (py) and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">⑥</span> (NH<sub>3</sub>). The reference axis of the octahedron connects the highest priority ligand with the lowest priority ligand <i>trans</i> to it. In the case of [PtBrClI(NH<sub>3</sub>)(NO<sub>2</sub>)(py)], there is only one priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> ligand, so the reference axis is <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—③</span> (I—Cl), and the first digit of the configuration index is ‘3’. The priority number of the ligand <i>trans</i> to the highest priority ligand in the plane that is <i>perpendicular</i> to the reference axis defines the second digit of the configuration index. In our case, NO<sub>2</sub> is <i>trans</i> to Br, therefore the second digit of the configuration index is ‘4’. Now we look at the ligands in this plane from the side of priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> ligand, i.e. iodine. We arrange the ligands in the numerical sequence starting from the highest priority atom. There are two possibilities, <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②–⑤–④–⑥</span> and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②–⑥–④–⑤</span>; since <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">⑤</span> > <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">⑥</span>, the former sequence, as “the lowest numerical sequence”, is preferred<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>. In the diagram on the left, the sequence <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②–⑤–④–⑥</span> goes anticlockwise; accordingly, the complete descriptor for this structure will be ‘<i>OC</i>-6-34-<i>A</i>’ and the full name (<i>OC</i>-6-34-<i>A</i>)-<span style="background-color: lightgreen;">amminebromidochloridoiodidonitrito-κ<i>N</i>-(pyridine)</span><span style="background-color: gold;">platinum</span>(<small>IV</small>). In the structure on the right, the sequence <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②–⑤–④–⑥</span> goes clockwise, thus (<i>OC</i>-6-34-<i>C</i>)-<span style="background-color: lightgreen;">amminebromidochloridoiodidonitrito-κ<i>N</i>-(pyridine)</span><span style="background-color: gold;">platinum</span>(<small>IV</small>). </p>
<p> Even though the <i>R</i>/<i>S</i> and <i>C</i>/<i>A</i> conventions deal with the same concept — viz. that of clockwise or anticlockwise arrangement of the ligands at the chiral centre according to the CIP rules — their practical uses differ significantly. The necessity to use the polyhedral symbol and configuration index in addition to the ‘<i>C</i>’ or ‘<i>A</i>’ descriptor effectively restrict the use of the <i>C</i>/<i>A</i> convention to the mononuclear coordination entities. Imagine how cumbersome the name like (2<i>R</i>,3<i>S</i>,4<i>R</i>,5<i>R</i>)-2,3,4,5,6-pentahydroxyhexanal would become if we had to specify that every chiral atom in it is <i>T</i>-4! </p>
<a name="ΔΛ"></a>
<h3><small>Δ/Λ</small></h3>
<p> In the specific case of octahedral complexes containing bidentate ligands, another system, known as the <i>skew-lines convention</i>, is applied [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-9.3.4.11]. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36411" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="Λ-tris(1,10-phenanthroline)ruthenium(2+) (CHEBI:36411)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFjKZyFgLy7Q5UIU6G-NSkD_ThBx5-S_byv8lr2OE9ZkjJpR1xzSgRz3eRDQ_ypCshvhXojNOk26R4NBhdEhwxsbgujez1OicDhrjKT6f913z9eQ8p10vGbfck9C8v4ugbWSQcUoJv8qrEdco7wO-giCKC6A96GKG2OY8WeppBKMWFwetMS-IFQw/s1600/Lambda-%5BRu(phen)3%5D2+.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36410" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="Δ-tris(1,10-phenanthroline)ruthenium(2+) (CHEBI:36410)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWzO7Ah8Tzdb3ePpzveFjco_9m_uctVNNMq9VSSbizpyXzSBxa90CSIH6ky1fNR4q4B-F4BNEfcXLxOMJw3-rRobuOdnBi22H22Wd22AleL9m6HRA3C4MkJl9kF2DQV2886Y4oycfYFdJv_U2-7bV8z_CZYAviMPB0SLeZJYeJpZ0URk3isSE-FA/s1600/Delta-%5BRu(phen)3%5D2+.png" width="200" /></a></td></tr>
<tr><th align="center">(h)</th> <th align="center">(i)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="8" type="a">
<li> Λ-tris(1,10-phenanthroline-κ<sup>2</sup><i>N</i><sup>1</sup>,<i>N</i><sup>10</sup>)ruthenium(2+) (<i>additive</i>) <br />
Λ-[Ru(phen)<sub>3</sub>]<sup>2+</sup> (<i>additive, abbreviated</i>) </li>
<li> Δ-tris(1,10-phenanthroline-κ<sup>2</sup><i>N</i><sup>1</sup>,<i>N</i><sup>10</sup>)ruthenium(2+) (<i>additive</i>) <br />
Δ-[Ru(phen)<sub>3</sub>]<sup>2+</sup> (<i>additive, abbreviated</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> The skew-lines are defined by the donor atoms of the ligands. In the case of structures <b>(h)</b> and <b>(i)</b>, the enantiomers of <span style="background-color: lightgreen;">tris(1,10-phenanthroline-κ<sup>2</sup><i>N</i><sup>1</sup>,<i>N</i><sup>10</sup>)</span><span style="background-color: gold;">ruthenium</span>(2+), the donor atoms are nitrogens, so we have three N—N lines. If you play with a <a href="https://chemapps.stolaf.edu/jmol/jmol.php?source=https://dl.dropboxusercontent.com/scl/fi/wqdnh36ydfxz6a3lvpf80/ChEBI_36411_3D.mol?rlkey=60306zux9d9ccrfplozahhqaq&dl=0" target="_blank" title="3-D structure of Λ-tris(1,10-phenanthroline)ruthenium(2+) (CHEBI:36411)">3-D structure</a> of <b>(e)</b>, you’ll discover that, no matter what you do, if you make any of the two N—N lines visually cross, with the intersection point more or less in the centre of the lines, the upper one always appears to be rotated approximately 60° <i>anticlockwise</i> relative to the lower one. This arrangement could be thought of as a left-handed helix and is assigned the Λ (lambda) descriptor, from the Ancient Greek <a href="http://en.wiktionary.org/wiki/%CE%BB%CE%B1%CE%B9%CF%8C%CF%82" title="λαιός in Wiktionary">λαιός</a>, “left-handed”. The complete name of <b>(h)</b> will be Λ-<span style="background-color: lightgreen;">tris(1,10-phenanthroline-κ<sup>2</sup><i>N</i><sup>1</sup>,<i>N</i><sup>10</sup>)</span><span style="background-color: gold;">ruthenium</span>(2+). On the contrary, with <a href="https://chemapps.stolaf.edu/jmol/jmol.php?source=https://dl.dropboxusercontent.com/scl/fi/uytgj5aqs6b1ct9cdogyo/ChEBI_36410_3D.mol?rlkey=tcftgk4pto7lz5f21c05k2u6l&dl=0" target="_blank" title="3-D structure of Δ-tris(1,10-phenanthroline)ruthenium(2+) (CHEBI:36410)">its enantiomer</a>, the upper of any two intersecting N—N lines always appears to be rotated <i>clockwise</i> relative to the lower one. This isomer is assigned Δ (delta) descriptor, from the Ancient Greek <a href="http://en.wiktionary.org/wiki/%CE%B4%CE%B5%CE%BE%CE%B9%CF%8C%CF%82" title="δεξιός in Wiktionary">δεξιός</a>, “right-handed”, thus Δ-<span style="background-color: lightgreen;">tris(1,10-phenanthroline-κ<sup>2</sup><i>N</i><sup>1</sup>,<i>N</i><sup>10</sup>)</span><span style="background-color: gold;">ruthenium</span>(2+). </p>
<p> Constable (2021) notes that using the <i>C</i>/<i>A</i> convention for tris(bidentate) complexes brings about the descriptors with different meaning of “clockwise” and “anticlockwise” compared to that of Δ and Λ [<a href="#Constable_2021" title="Constable (2021)">5</a>, <a href="http://www.mdpi.com/2073-8994/13/10/1891#symmetry-13-01891-f016" target="_blank" title="Constable (2021), Figure 16">Fig. 16</a>]. This is because all the donor atoms have the same priority and to differentiate them, the priming convention is used [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-9.3.5.3]. The pairs of donor atoms in each bidentate ligand are arbitrarily unprimed, primed, or double primed. Since the priorities are <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> > <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′</span> > <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①″</span>, the reference axis of the octahedron is <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—①″</span>. The atoms left in the plane perpendicular to it have priorities <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span>, <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′</span>, <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①′</span> and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①″</span>. The numerical sequence <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①–①′–①′–①″</span> goes clockwise in Λ isomer and anticlockwise in Δ isomer, giving (<i>OC</i>-6-1″1′-<i>C</i>) for Λ and (<i>OC</i>-6-1″1′-<i>A</i>) for Δ. Confused? I bet you are. Personally, I prefer more tangible helicity of the Δ/Λ system to the arbitrary handedness of the <i>C</i>/<i>A</i> convention. </p>
<a name="PM"></a>
<h3><small><i>P</i>/<i>M</i></small></h3>
<p> Some molecules do not have any chiral centres and yet are chiral. Observe <b>(j)</b> and <b>(k)</b>, two enantiomers of <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33150" target="_blank" title="hexahelicene (CHEBI:33150)">hexahelicene</a>: </p>
<center>
<table>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh58o_vNrrufut6K86fM6gfkpU0I9mknUgaOsNty2yMeMaQmOa9GWGhdjWxfPF74G1vQKW3uQiiAD7GDRUjUFNB-HatGYNq1BFNMoTq9KY8AvPThOiBnXWgPDJ2EtCzxED5gBEKUDmgcldOIxnokqFgMJTQgmhoxITBe8kWUXRLoaMDZIyBh-q3SA/s500/P-hexahelicene.png" style="margin-left: 1em; margin-right: 1em;" title="(P)-hexahelicene"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh58o_vNrrufut6K86fM6gfkpU0I9mknUgaOsNty2yMeMaQmOa9GWGhdjWxfPF74G1vQKW3uQiiAD7GDRUjUFNB-HatGYNq1BFNMoTq9KY8AvPThOiBnXWgPDJ2EtCzxED5gBEKUDmgcldOIxnokqFgMJTQgmhoxITBe8kWUXRLoaMDZIyBh-q3SA/w200-h200/P-hexahelicene.png" width="200" /></a></td>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpDRsGYgWpfpCFTy8Tmh6UDycfLCQ6fQiiWU14CZ6gU7aeFrR_MM083Dqzh94ktxjKyNj0FV_xccx2CEJUlNwySuQLxsJC5f1t2p7hebSIp9kCo4r1o2RuzEyFg2dWOwSr1Gtyh4i0WSCHZaiJdUotSWnYqLgjsyv2Wyl_P4h1UQMjKRQoxWYLUQ/s500/M-hexahelicene.png" style="margin-left: 1em; margin-right: 1em;" title="(M)-hexahelicene"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpDRsGYgWpfpCFTy8Tmh6UDycfLCQ6fQiiWU14CZ6gU7aeFrR_MM083Dqzh94ktxjKyNj0FV_xccx2CEJUlNwySuQLxsJC5f1t2p7hebSIp9kCo4r1o2RuzEyFg2dWOwSr1Gtyh4i0WSCHZaiJdUotSWnYqLgjsyv2Wyl_P4h1UQMjKRQoxWYLUQ/w200-h200/M-hexahelicene.png" width="200" /></a></td></tr>
<tr><th align="center">(j)</th> <th align="center">(k)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="10" type="a">
<li> (<i>P</i>)-hexahelicene (<i>PIN</i>) </li>
<li> (<i>M</i>)-hexahelicene (<i>PIN</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> You don’t need any seniority rules to see that the structure <b>(j)</b> is a right-handed helix and <b>(k)</b> is a left-handed helix. Their chirality is indicated by the stereodescriptors ‘<i>P</i>’ (“plus”) and ‘<i>M</i>’ (“minus”), respectively [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#9201020201" target="_blank" title="Blue Book, P-92.1.2.2.1">P-92.1.2.2.1</a>]. </p>
<p> The descriptors ‘<i>M</i>’ and ‘<i>P</i>’ also could be used to specify chirality of compounds such as <a href="http://metallome.blogspot.com/2023/12/axial-chirality.html" title="Axial chirality @ this blog" target="_blank">allenes and hindered biaryls</a>, however in these cases you have to apply the CIP rules. </p>
<p> To sum up: </p>
<ul> <li> The concepts of right- and left-handedness in chemical names are conveyed by a variety of conventions: <a href="#(+)(−)" title="(+)/(−)">(+)/(−)</a>, <a href="#PM" title="P/M"><i>P</i>/<i>M</i></a> (plus/minus), <i>d</i>/<i>l</i>, <a href="#DL" title="D/L"><small>D</small>/<small>L</small></a> (<i>dexter</i>/<i>laevus</i>), <a href="#ΔΛ" title="Δ/Λ">Δ/Λ</a> (δεξιός/λαιός), <a href="#RS" title="R/S"><i>R</i>/<i>S</i></a> (<i>rectus</i>/<i>sinister</i>), <a href="#CA" title="C/A"><i>C</i>/<i>A</i></a> (clockwise/anticlockwise). </li>
<li> Descriptors ‘(+)’, ‘(−)’, ‘<i>d</i>’, ‘<i>l</i>’, ‘<i>rac</i>’ or ‘(±)’ refer to optical activity in a macroscopic system but don’t tell us anything about molecular geometry. </li>
<li> The descriptors ‘<i>R</i>’ and ‘<i>S</i>’ define the absolute configuration at tetrahedral and trigonal pyramidal chiral centres using the CIP sequence rules. </li>
<li> The descriptors ‘<i>C</i>’ and ‘<i>A</i>’ define the absolute configuration at other polyhedral chiral centres using the CIP sequence rules. </li>
<li> The descriptors ‘<small>D</small>’ and ‘<small>L</small>’ are assigned to the whole molecule according to the absolute configuration of one special chiral centre, aka configurational atom. The configurations of other centres relative to the configurational atom are defined by “configurational prefixes” such as <i>gluco</i>, <i>erythro</i>, <i>threo</i>, <i>ribo</i>, etc. This system is used in nomenclature of carbohydrates, amino acids and cyclitols. </li>
<li> The descriptors ‘Δ’ and ‘Λ’ describe configurations of octahedral complexes containing bidentate ligands. </li>
<li> The descriptors ‘<i>M</i>’ and ‘<i>P</i>’ describe configurations of molecules that lack chiral atoms. </li>
</ul>
<h3><small>Closing remarks</small></h3>
<p> None of these symbols are particularly original. Italicised element symbols ‘<i>C</i>’, ‘<i>P</i>’ and ‘<i>S</i>’ are used in both inorganic and organic nomenclature [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-2.9; <a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P1.html#160602" target="_blank" title="Blue Book, P-16.6.2">P-16.6.2</a>]. The symbol ‘Δ’ is used in organic nomenclature for localised double bonds [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P2.html#25070102" target="_blank" title="Blue Book, P-25.7.1.2">P-25.7.1.2</a>] and still widely employed by biochemists to indicate unsaturation in lipids. The capital ‘D’ (although not the small cap ‘<small>D</small>’, but honestly, how many people see the difference?) is a symbol for deuterium. If I were to propose a new stereochemical notation now, I would go for ‘↺’ (anticlockwise open circle arrow, Unicode <a href="http://unicode.org/cldr/utility/character.jsp?a=21BA" target="_blank" title="U+21BA">U+21BA</a>) and ‘↻’ (clockwise open circle arrow, Unicode <a href="http://unicode.org/cldr/utility/character.jsp?a=21BB" target="_blank" title="U+21BB">U+21BB</a>). That’s how our names would look like: </p>
<ul>
↻-glyceraldehyde <b>(g)</b> <br />
(2↻,3↺,4↻,5↻)-2,3,4,5,6-pentahydroxyhexanal <b>(e)</b> <br />
(<i>OC</i>-6-34-↻)-amminebromidochloridoiodidonitrito-κ<i>N</i>-(pyridine)platinum(<small>IV</small>) <br />
↺-[Ru(phen)<sub>3</sub>]<sup>2+</sup> <b>(h)</b> <br />
↻-hexahelicene <b>(j)</b>
</ul>
<p> Beautiful. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> Of course, “right” is not the same as “clockwise”. Clock hands go from left to right only half of the time, from 9 to 3 o’clock (and right to left the other half of the time). Likewise, if the plane of polarisation rotates clockwise, it’s dextrorotating only half of the time. The chirality rules really rely on concepts of “clockwise” and “anticlockwise”, not “right” and “left”. It’s unfortunate that the confusion lives in chemical nomenclature. </td></tr>
<tr><td valign="top">†</td>
<td> On top of the confusion between “right” and “clockwise”, the descriptor ‘<i>R</i>’ is based on wrong etymology. The Latin word <a href="http://en.wiktionary.org/wiki/rectus#Latin" target="_blank" title="rectus in Wiktionary"><i>rectus</i></a> means “right” but in a sense “straight”, “upright”, i.e. “not curved”. It does not imply the “right-hand” direction at all. Thus <i>rectus</i> is a different “right” compared to <a href="http://en.wiktionary.org/wiki/dexter#Latin" target="_blank" title="dexter in Wiktionary"><i>dexter</i></a>, which indeed is the opposite of “left”. </td></tr>
<tr><td valign="top">‡</td>
<td> “The lowest numerical sequence is that having the lower number at the first point of difference when the numbers are compared digit by digit from one end to the other” [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-9.3.3.6]. </td>
</tr>
</table>
<h4>References</h4>
<ol>
<a name="Cross_and_Klyne_1976"></a>
<li> Cross, L.C. and Klyne, W. (1976) Nomenclature of Organic Chemistry. Section E: Stereochemistry (Recommendations 1974). <a href="http://publications.iupac.org/pac/1976/pdf/4501x0011.pdf" target="_blank" title="Pure Appl. Chem. 45, 11-30."><i>Pure and Applied Chemistry</i> <b>45</b>, 11—30</a>. </li>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
<a name="Blue_Book_2014"></a>
<li>Favre, H.A. and Powell, W.H. <a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
<a name="McNaught_1996"></a>
<li> McNaught, A.D. (1996) Nomenclature of carbohydrates (IUPAC recommendations 1996). <a href="http://doi.org/10.1351/pac199668101919" target="_blank" title="McNaught (1996) Pure Appl. Chem. 68, 1919-2008."><i>Pure and Applied Chemistry</i> <b>68</b>, 1919—2008</a>. </li>
<a name="Constable_2021"></a>
<li> Constable, E.C. (2021) Through a glass darkly — Some thoughts on symmetry and chemistry. <a href="http://doi.org/10.3390/sym13101891" target="_blank" title="Constable (2021) Symmetry 13, 1891."><i>Symmetry</i> <b>13</b>, 1891</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-17814615935485637902023-08-07T19:00:00.041+01:002023-12-09T00:09:07.914+00:00Polyhedral symbols and configuration indices<link href="http://fonts.googleapis.com/css?family=Noto+Sans+Symbols" rel="stylesheet" type="text/css"></link>
<link href="http://fonts.googleapis.com/css?family=Noto+Sans+Japanese" rel="stylesheet" type="text/css"></link>
<link href="http://fonts.googleapis.com/css?family=Overpass" rel="stylesheet" type="text/css"></link>
<link href="http://fonts.googleapis.com/css?family=Inter" rel="stylesheet" type="text/css"></link>
<link href="http://fonts.googleapis.com/css?family=M+PLUS+Rounded+1c" rel="stylesheet" type="text/css"></link>
<link href="http://fonts.googleapis.com/css?family=M+PLUS+1p" rel="stylesheet" type="text/css"></link>
<p> Although structural descriptors such as we’ve seen in the names of <a href="http://metallome.blogspot.com/2023/06/boron-hydride-nomenclature.html" target="_blank" title="Boron hydride nomenclature in Wikipedia">boron hydrides</a>, for example <a href="http://goldbook.iupac.org/terms/view/C00903" target="_blank" title="catena- in Gold Book"><i>catena</i></a> or <a href="http://goldbook.iupac.org/terms/view/C01106" target="_blank" title="closo- in Gold Book"><i>closo</i></a>, provide information on atomic connectivity, they tell us little or nothing about the geometry of the molecule. </p>
<p> Have a look at the structures <b>(a)</b> and <b>(b)</b>: </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:46449" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(SPY-5)-pentaoxotungstate(4−) (CHEBI:46449)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQANCednKmVQq8qfQdb7GKFvZan_kTvG8uPmbO8F58grRcRwgpChqk93aNEorN3D00RiHPmHvK3Q-h2HjPPc7s-hBU5Z2EvJIyaYe_FNpxoLYJriET5IXmT6NtVq-cNikSHnsZjAHLk1pJaT97lzs2Ui5FlshDjaPjcoydO7k0snLgN-e4jaheJg/s1600/SPY-5-pentaoxotungstate.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:46639" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(TBPY-5)-pentaoxotungstate(4−) (CHEBI:46639)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3Wcwy6AtOwwPKoDzQvtQxSZogxyvozBhMIgXPDEDoaiGWJBGGwXiqNH9SfoRqMjYmaI-FWbqxCnvu_o1qnW9AwdXWqzuQOD5fqTw6E077lcBvuyiXAvo-t65eZi2hwdoNdnw6KpC3GWTR0acsfZqAreNIPcXgog1ZjAUR6XfEWKkAd1QfoyNzFw/s1600/TBPY-5-pentaoxotungstate.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> (<i>SPY</i>-5)-pentaoxidotungstate(4−) (<i>additive</i>) </li>
<li> (<i>TBPY</i>-5)-pentaoxidotungstate(4−) (<i>additive</i>)</li>
</ol>
</td></tr>
</table>
</center>
<p> Both of them can be named <a href="http://metallome.blogspot.com/2020/06/addictive-names.html" target="_blank" title="Addi(c)tive names @ this blog">additively</a> <span style="background-color: lightgreen;">pentaoxido</span><span style="background-color: gold;">tungstate</span>(4−). Yet, as you can see, they have very different shapes.
<a name='more'></a>
We can tell one from another with the help of special descriptors known as <a href="http://goldbook.iupac.org/terms/view/PT06792" target="_blank" title="polyhedral symbol in Gold Book"><i>polyhedral symbols</i></a>. The molecule <b>(a)</b> adopts a pentacoordinate square pyramidal (<i>SPY</i>-5) geometry, while <b>(b)</b> is a pentacoordinate trigonal bipyramid (<i>TBPY</i>-5). Therefore, their corresponding — and more informative — names will be (<i>SPY</i>-5)-<span style="background-color: lightgreen;">pentaoxido</span><span style="background-color: gold;">tungstate</span>(4−) and (<i>TBPY</i>-5)-<span style="background-color: lightgreen;">pentaoxido</span><span style="background-color: gold;">tungstate</span>(4−). </p>
<p> For coordination numbers 2 to 9, IUPAC recommends the following polyhedral symbols [<a href="#Red_Book_2005" title="Red Book (2005)">1</a>, IR-9.3.2.1, Table IR-9.2]:
</p>
<table border="0" cellpadding="3" cellspacing="1" style="width: 100%;">
<tr>
<th> Coordination polyhedron </th>
<th align="center"> Coordination number </th>
<th> Polyhedral symbol </th>
</tr>
<tr>
<td> Angular </td>
<td align="center"> 2 </td>
<td> <i>A</i>-2 </td>
</tr>
<tr>
<td> Linear </td>
<td align="center"> 2 </td>
<td> <i>L</i>-2 </td>
</tr>
<tr>
<td> Trigonal plane </td>
<td align="center"> 3 </td>
<td> <i>TP</i>-3 </td>
</tr>
<tr>
<td> Trigonal pyramid </td>
<td align="center"> 3 </td>
<td><i>TPY</i>-3</td>
</tr>
<tr>
<td> T-shape </td>
<td align="center"> 3 </td>
<td> <i>TS</i>-3 </td>
</tr>
<tr>
<td> Square plane </td>
<td align="center">4</td>
<td> <i>SP</i>-4 </td>
</tr>
<tr>
<td> Square pyramid </td>
<td align="center"> 4 </td>
<td> <i>SPY</i>-4 </td>
</tr>
<tr>
<td> See-saw </td>
<td align="center"> 4 </td>
<td> <i>SS</i>-4 </td>
</tr>
<tr>
<td> Tetrahedron </td>
<td align="center">4</td>
<td> <i>T</i>-4 </td>
</tr>
<tr>
<td> Square pyramid </td>
<td align="center"> 5 </td>
<td> <i>SPY</i>-5 </td>
</tr>
<tr>
<td> Trigonal bipyramid </td>
<td align="center"> 5 </td>
<td> <i>TBPY</i>-5 </td>
</tr>
<tr>
<td> Octahedron </td>
<td align="center"> 6 </td>
<td> <i>OC</i>-6 </td>
</tr>
<tr>
<td> Trigonal prism </td>
<td align="center"> 6 </td>
<td> <i>TPR</i>-6 </td>
</tr>
<tr>
<td> Octahedron, face monocapped </td>
<td align="center"> 7 </td>
<td> <i>OCF</i>-7 </td>
</tr>
<tr>
<td> Pentagonal bipyramid </td>
<td align="center"> 7 </td>
<td> <i>PBPY</i>-7 </td>
</tr>
<tr>
<td> Trigonal prism, square face monocapped </td>
<td align="center"> 7 </td>
<td> <i>TPRS</i>-7 </td>
</tr>
<tr>
<td> Cube </td>
<td align="center"> 8 </td>
<td> <i>CU</i>-8 </td>
</tr>
<tr>
<td> Dodecahedron </td>
<td align="center"> 8 </td>
<td> <i>DD</i>-8 </td>
</tr>
<tr>
<td> Hexagonal bipyramid </td>
<td align="center"> 8 </td>
<td> <i>HBPY</i>-8 </td>
</tr>
<tr>
<td> Octahedron, <i>trans</i>-bicapped </td>
<td align="center"> 8 </td>
<td> <i>OCT</i>-8 </td>
</tr>
<tr>
<td> Square antiprism </td>
<td align="center"> 8 </td>
<td> <i>SARP</i>-8 </td>
</tr>
<tr>
<td> Trigonal prism, square-face bicapped </td>
<td align="center"> 8 </td>
<td> <i>TPRS</i>-8 </td>
</tr>
<tr>
<td> Trigonal prism, triangular-face bicapped </td>
<td align="center"> 8 </td>
<td> <i>TPRT</i>-8 </td>
</tr>
<tr>
<td> Heptagonal bipyramid </td>
<td align="center"> 9 </td>
<td> <i>HBPY</i>-9 </td>
</tr>
<tr>
<td> Trigonal prism, square-face tricapped </td>
<td align="center"> 9 </td>
<td> <i>TPRS</i>-9 </td>
</tr>
</table>
<p> <a href="http://metallome.blogspot.com/p/polyhedral-symbols.html" target="_blank" title="Polyhedral symbols @ this blog">More polyhedral symbols</a> have been proposed for higher coordination numbers [<a href="#Hartshorn_2007" title="Hartshorn et al. (2007)">2</a>]. In organic compounds, commonly encountered polyhedra include <i>TPY</i>-3, <i>TS</i>-3, <i>T</i>-4, <i>SP</i>-4, <i>SS</i>-4, <i>TBPY</i>-5, <i>SPY</i>-5 and <i>OC</i>-6 [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#930302" target="_blank" title="Blue Book, P-93.3.2">P-93.3.2</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#t901" target="_blank" title="Blue Book, Table 9.1">Table 9.1</a>]; the symbol (<i>T</i>-4) — tetrahedron being the default coordination polyhedron for carbon — is not used in organic nomenclature [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#93030302" target="_blank" title="Blue Book, P-93.3.3.2">P-93.3.3.2</a>]. </p>
<p> Let us represent the coordination complexes in the form [Ma<sub><i>i</i></sub>b<sub><i>j</i></sub>...], where M is the central atom, ‘a’, ‘b’, etc. are different types of ligands, and <i>i</i>, <i>j</i>, etc. indicate the number of ligands. For complexes of the form [Ma<sub><i>i</i></sub>], that is, if all the ligands are the same, as is the case with structures <b>(a)</b>—<b>(c)</b><sup><a href="#Footnote_*" title="Footnote *">*</a></sup>, there is no need to add anything to the polyhedral symbol. Ditto for [Ma<sub><i>i</i></sub>b<sub>1</sub>] , i.e. if only <i>one</i> ligand of type ‘b’ is present in polyhedra such as <i>T</i>-4, <i>SP</i>-4 and <i>OC</i>-6, as in the case of (<i>OC</i>-6)-amminepentacyanidoferrate(3−) <b>(d)</b>. But for [Ma<sub><i>i</i></sub>b<sub><i>j</i></sub>] (where <i>i</i>>1, <i>j</i>>1), that is, if we add <i>another</i> ligand of type ‘b’, the situation could change dramatically. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30118" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tetrachloroplatinate(2−) (CHEBI:30118)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDgvD08GM01riSrC1SB7E1AjmqFli95dzNQ_88ow2U9WglyZktQyibECVOTok1Q_6uE4mRDrhUhWul-8n3ohnMSyDT76V9nkoPana3MtascZi3silzZGIa5BeFt_iswVYeTI5piujkbdoarcaMRi1zsspNpb2wWuzCoSr2xnxyXasSzVAN2CChrA/s1600/tetrachloroplatinate.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30998" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="amminepentacyanoferrate(3−) (CHEBI:30998)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBqJ0FtsGjPCpdPwLaWaXZvIlElQ-8HyUVbyWPo8X49efZtXvu3SECpnGrC0hGEkMiqRAs-grsRT-C3eVZVXsYlXzqa-9DJMU3ixxOaXO_87IyAJXLk6ARjnYrjhZyjhjd3pXj2UusBY5pt_43IzIhmymTPF_jPGE1TTRfc0mDZ0DLY9MLbRaQrw/s1600/amminepentacyanoferrate.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> (<i>SP</i>-4)-tetrachloridoplatinate(2−) (<i>additive</i>) </li>
<li> (<i>OC</i>-6)-amminepentacyanidoferrate(3−) (<i>additive</i>) </li>
</ol>
</td></tr>
</table>
</center>
<a name="cis-trans">
<p> Consider the isomers <b>(e)</b> and <b>(f)</b>. The complex <b>(e)</b> is known as <a href="http://en.wikipedia.org/wiki/Cisplatin" target="_blank" title="Cisplatin in Wikipedia">cisplatin</a> and is used to treat some types of cancer. Its isomer <b>(f)</b>, <a href="http://en.wikipedia.org/wiki/Transplatin" target="_blank" title="Transplatin in Wikipedia">transplatin</a>, does not show comparable anticancer activity. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27899" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cisplatin (CHEBI:27899)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMObDsqXO61dwVMywMfxOHqvn8JWxxzl6rEuhGW-B7ufNfDi6k9wx4Fl5E6feliq3Z5g16Ag4TA8tF4sIHfeyhnlOIuWNuAznkkiD7SnE9VPR5jew_Vh0BuIZ2cwqZ0D2OFscM2wOMzTw8Z0y5w_0wB6Dn6f15JCJqcP8VpQu0UmMrCMTlgVowNg/s1600/cisplatin.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35852" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="transplatin (CHEBI:35852)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh78eDqCemRgsqUtkAgfA5SAf6IghBqasGy7SkJxsHFsk0zwpf8XdPlqN-bu9M6FDgsPlsUJ2AQ_Vq_MimYPvHvszntaUzjegLzpDgn6Rz1rEFuU8HRo1rBTgzlYylnPWhlhBya7QhSW_T93UxfIP34ueO7DH1KXIw6oZRiqF0A2oFTQJpTG6Bqow/s1600/transplatin.png" width="200" /></a></td></tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> cisplatin (<i>INN</i>) <br />
<i>cis</i>-diamminedichloridoplatinum(<small>II</small>) (<i>additive</i>) <br />
(<i>SP</i>-4-2)-diamminedichloridoplatinum (<i>additive</i>) <br />
</li>
<li> transplatin (<i>trivial</i>) <br />
<i>trans</i>-diamminedichloridoplatinum(<small>II</small>) (<i>additive</i>) <br />
(<i>SP</i>-4-1)-diamminedichloridoplatinum (<i>additive</i>) <br />
</li>
</ol>
</td></tr>
</table>
</center>
<p> Square planar complexes of the form [Ma<sub>2</sub>b<sub>2</sub>] are commonly differentiated by the descriptors <i>cis</i> and <i>trans</i> [<a href="#Red_Book_2005" title="Red Book (2005)">1</a>, IR-9.3.3.3], so <b>(e)</b> and <b>(f)</b> can be called <i>cis</i>-<span style="background-color: lightgreen;">diamminedichlorido</span><span style="background-color: gold;">platinum</span>(<small>II</small>) and <i>trans</i>-<span style="background-color: lightgreen;">diamminedichlorido</span><span style="background-color: gold;">platinum</span>(<small>II</small>), respectively. However, if we need to distinguish between isomers of the form [Mabcd], or if we want to use (<i>SP</i>-4) symbol, we can follow a more general procedure recommended by IUPAC [<a href="#Red_Book_2005" title="Red Book (2005)">1</a>, IR-9.3.3.3]. </p>
<p> Each donor atom in the complex is assigned a priority number according to the <a href="http://en.wikipedia.org/wiki/Cahn%E2%80%93Ingold%E2%80%93Prelog_priority_rules" target="_blank" title="Cahn–Ingold–Prelog priority rules in Wikipedia">Cahn–Ingold–Prelog</a> (CIP) sequence rules. These priority numbers are then used to form the <i>configuration index</i> which is the single digit corresponding to the priority number of the donor atom <i>trans</i> to the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> donor. The configuration index follows the polyhedral symbol (<i>SP</i>-4). In case of <b>(e)</b>, the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②</span> atom (nitrogen) is <i>trans</i> to the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> atom (chlorine), so the configuration index will be ‘2’: (<i>SP</i>-4-2)-<span style="background-color: lightgreen;">diamminedichlorido</span><span style="background-color: gold;">platinum</span>, while for <b>(f)</b>, the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> atoms (chlorine) are <i>trans</i> to each other, thus the configuration index is ‘1’: (<i>SP</i>-4-1)-<span style="background-color: lightgreen;">diamminedichlorido</span><span style="background-color: gold;">platinum</span>. </p>
<p> Similar rules are used to name octahedral systems, although the configuration index now consists of <i>two</i> digits that follow the polyhedral symbol (<i>OC</i>-6) [<a href="#Red_Book_2005" title="Red Book (2005)">1</a>, IR-9.3.3.4]. Let’s see how it works with the isomers <b>(g)</b> and <b>(h)</b>. Warning: it can get a bit tedious; feel free <a href="#Last_Paragraph" title="the last paragraph">to skip it</a>. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30693" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cis-tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)molybdenum (CHEBI:30693)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1oUg5vrmN_UxH5L9NBTkSiCeQIZLVsQtGMuFPoy7-VdmH4aANdz6MJNjcyeqOMtGTF_RTd2PKB-yZFrTz9UvFuzSLLQ-9EQ9kT6gOqB9-F3jEUCB_D9eHD7hD01NyhEISqHBqu4WUmSDlw0a3JW1xXm0bBJILwYCkFMkvj9NpEnBc1X042yKHcg/s1600/cis-%5BMo(N2)2(PMe2Ph)4%5D.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30694" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="trans-tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)molybdenum (CHEBI:30694)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZpSjnWwTscOML5En91wrEsEJL9w0t-0OwOMswVFX2VCLueT4D6x-BRANQS_6-EcEeDfrmoAHWVcoZg2rwHFcQd3rX4jd2fec1p7exr26jE6Hti_K1mO30U0YszWcy2q0ai4Q2Zuncmal9Z4GXh2gSokgpN608jNU_AmHYd4fdUPAGirbwOuSp8g/s1600/trans-%5BMo(N2)2(PMe2Ph)4%5D.png" width="200" /></a></td></tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> (<i>OC</i>-6-22)-tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)molybdenum (<i>additive</i>) <br />
<i>cis</i>-[Mo(N<sub>2</sub>)<sub>2</sub>(PMe<sub>2</sub>Ph)<sub>4</sub>] (<i>additive, abbreviated</i>) </li>
<li> (<i>OC</i>-6-11)-tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)molybdenum (<i>additive</i>) <br />
<i>trans</i>-[Mo(N<sub>2</sub>)<sub>2</sub>(PMe<sub>2</sub>Ph)<sub>4</sub>] (<i>additive, abbreviated</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> First, let’s assign the priority numbers. There are only two types of ligands in <b>(g)</b> and <b>(h)</b> to the central <span style="background-color: gold;">molybdenum</span> atom: <span style="background-color: lightgreen;">dimethyl(phenyl)phosphane</span> and <span style="background-color: lightgreen;">dinitrogen</span>. According to the CIP rules, the priority numbers for their respective donor atoms are <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> (phosphorus) and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②</span> (nitrogen). </p>
<p> The pairs of donor atoms at the opposite vertices of an octahedron are said to be <i>trans</i> to each other. There are three <i>C</i><sub>4</sub> <a href="http://en.wikipedia.org/wiki/Molecular_symmetry" target="_blank" title="Molecular symmetry in Wikipedia">symmetry axes</a> passing through these vertices. The <i>reference axis</i> of the octahedron is the one connecting the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> atom and the <i>lowest</i> priority (and therefore <i>highest</i> numerical value) atom <i>trans</i> to it. In <b>(g)</b>, there are two identical axes <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—②</span> (phosphorus—nitrogen), so we can choose either of them as a reference axis. </p>
<p> The reference axis will give us the <b>first digit</b> of the configuration index: it is the priority number of the donor atom <i>trans</i> to the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> donor atom. In case of <b>(g)</b>, the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②</span> (N) is <i>trans</i> to the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> atom (P), so the first digit of the configuration index is ‘2’. </p>
<p> The <b>second digit</b> of the configuration index is the priority number of the donor atom <i>trans</i> to the most preferred donor atom in the plane that is <i>perpendicular</i> to the reference axis. If there is a choice, the lowest priority (highest numerical value) number is selected. For <b>(g)</b>, in the plane perpendicular to the reference axis <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—②</span>, we have two other axes: <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—②</span> (P—N) and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—①</span> (P—P). We choose the priority number which has the highest numerical value, i.e. <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②</span>. Thus the configuration index for <b>(g)</b> is ‘22’ and the complete name will be (<i>OC</i>-6-22)-<span style="background-color: lightgreen;">tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)</span><span style="background-color: gold;">molybdenum</span>. </p>
<p> In case of <b>(h)</b>, the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> atoms (P) are always <i>trans</i> to each other, so the two reference axes are <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—①</span> and the first digit of the configuration index will be ‘1’. In the plane perpendicular to the reference axis <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—①</span> there are two other axes: <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①—①</span> (P—P) and <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">②—②</span> (N—N). Since the atom <i>trans</i> to the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span> atom also has the priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">①</span>, the second digit is ‘1’ and the configuration index for <b>(h)</b> will be ‘11’, thus (<i>OC</i>-6-11)-<span style="background-color: lightgreen;">tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)</span><span style="background-color: gold;">molybdenum</span>. </p>
<a name="Last_Paragraph">
<p> The Red Book also provides the rules for <i>TS</i>-3, <i>SS</i>-4, <i>SPY</i>-4, <i>SPY</i>-5, <i>TBPY</i>-5, <i>PBPY</i>-7, <i>HBPY</i>-8 and <i>HBPY</i>-9 systems [<a href="#Red_Book_2005" title="Red Book (2005)">1</a>, pp. 183—185]. As you can imagine, the more vertices there are, the more complex the configuration index grows. For coordination numbers higher than 6, the configuration indices consist of <i>two</i> segments divided by a hyphen. Hartshorn <i>et al.</i> furnish an example descriptor ‘<i>SAPRS</i>-10-49-135827<u>10</u>6-<i>A</i>’, where <i>SAPRS</i>-10 is the proposed polyhedral symbol for decacoordinate square-face bicapped square antiprism, 49-135827<u>10</u>6 is the configuration index, and <i>A</i> is the absolute configuration stereodescriptor [<a href="#Hartshorn_2007" title="Hartshorn et al. (2007)">2</a>]. The authors thought it necessary to underscore ‘10’ in the configuration index “in order to avoid any ambiguity with two separate designators, 1 and 0”, although there is no such thing as priority <span style="font-family: 'Inter', 'M PLUS 1p', 'M PLUS Rounded 1c', 'Overpass', 'Noto Sans Japanese', 'Noto Sans Symbols';">⓪</span> atoms. Still, they have a point: for coordination numbers above 10, we’ll <i>need</i> a system to differentiate between one-digit and two-digit numbers, say by enclosing the latter in commas or something. Maybe there <i>is</i> a good reason why IUPAC didn’t recommend anything (so far) beyond coordination number 9. </p>
<a name="Footnote_*"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> See [<a href="#Blue_Book_2014" title="Blue Book (2014)">3</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P9.html#930302" target="_blank" title="Blue Book, P-93.3.2">P-93.3.2</a>] for more examples. </td></tr>
</table>
<h4>References</h4>
<ol>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
<a name="Hartshorn_2007"></a>
<li> Hartshorn, R.M., Hey-Hawkins, E., Kalio, R. and Leigh, G.J. (2007) Representation of configuration in coordination polyhedra and the extension of current methodology to coordination numbers greater than six (IUPAC Technical Report). <a href="http://doi.org/10.1351/pac200779101779" target="_blank" title="Pure Appl.Chem. 79, 1779–1799."><i>Pure and Applied Chemistry</i> <b>79</b>, 1779—1799</a>. </li>
<a name="Blue_Book_2014"></a>
<li><a name="Blue_Book_2014"> Favre, H.A. and Powell, W.H. </a><a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-56518311031817835982023-06-25T21:00:00.055+01:002023-09-03T10:38:05.540+01:00Boron hydride nomenclature<p> Can we expand the <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">parent hydride</a> naming philosophy much beyond organic chemistry? Not going too far, let’s have a peek at carbon’s immediate neighbour in the periodic table, boron. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30149" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="borane (CHEBI:30149)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNdM18t0fz246BtBNKPf_t9WoWg8qFsg4O8a0k2hGVBSz1_z2SOZMRuHIqXp4itIPoTgTRSC2TjHvtZ7Rlif-RheONYwvprZztpDeFhvtoOzZO-BX4BPTamImPmSJVq1buBdh9rjsZWZNOa4jCQOpiwhB7znK3YZ4ipTzW9K04XKL51LdH094/s16000/borane.png" /></a></td>
</tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> BH<sub>3</sub> <br />
borane (<i>preselected name</i>) <br />
boron trihydride (<i>binary</i>) <br />
trihydridoboron (<i>additive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The <a href="http://metallome.blogspot.com/p/parent-names-of-mononuclear-hydrides.html" target="_blank" title="Parent names of mononuclear hydrides @ this blog">mononuclear hydride</a> <b>(a)</b> is systematically named ‘borane’ while neutral boron hydrides as a class are called <a href="http://goldbook.iupac.org/terms/view/B00709" target="_blank" title="boranes in Gold Book"><i>boranes</i></a>. </p>
<a name='more'></a>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:38288" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="diborane(4) (CHEBI:38288)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEY2QOHXwkO6_E5Ykm3aMAHOoNoJQlGZeXLsYWkjoSboWJT3gYMMUSXRzoBg5kOonp41uPs7fPSnYDjo2V2y8HfdAEOm6cKkL8WFWzQAZsmB8ik03sWuGaKlXkBOXSUbgCpB8G3rigixrQ-VyF-HQ7k501jT1Z9hbyAUqchCksJSObpKOOc_8/s1600/diborane(4).png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33602" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="triborane(5) (CHEBI:33602)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAnELIY_TGZkJusMvjp8wsSHhAAqxM01NfK_Ez_tZNr22oAKJbX_X3fKdAOM-r38QpmibQKMeMxEnYzC66ALaZ_MmtN3nwMB0EDX0_OT6XJ9rI-jOQCBKs9PTMR1Jt3JCm9bmjnqO12lSmShYhy2xVJhWKJhot1s-XVaIzjJJfL0YTzpOClUE/s1600/triborane(5).png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33123" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclotetraborane (CHEBI:33123)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSEjJWtfM1AFAl52VmCJrXrC9TDJyW4iomBvgwd6YkqfwVaXUmFstUrsVTjPSIZfAzyEtxUa0DzLYH4w5Zz2dOTFGxv1vUiXsyOKYPtQqQ_LhjFmgnL-RF2AGG-ZdhlvdnOLYEqg/s0/cyclotetraborane.png" /></a></td>
</tr>
<tr><th align="center">(b)</th> <th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="2" type="a">
<li> B<sub>2</sub>H<sub>4</sub> <br />
H<sub>2</sub>B–BH<sub>2</sub> <br />
boranylborane (<i>boron hydride + substitutive</i>) <br />
diborane(4) (<i>boron hydride, preselected name</i>) </li>
<li> B<sub>3</sub>H<sub>5</sub> <br />
H<sub>2</sub>B–BH–BH<sub>2</sub> <br />
<i>catena</i>-triborane(5) (<i>boron hydride</i>) <br />
triborane(5) (<i>boron hydride, preselected name</i>) </li>
<li> B<sub>4</sub>H<sub>4</sub> <br />
cyclotetraborane(4) (<i>boron hydride</i>) <br />
tetraboretane (<i>Hantzsch-Widman, preselected name</i>)</li>
</ol></td></tr></table></center>
<p> Ignoring for a moment the number of hydrogen atoms, the structures <b>(b)</b>—<b>(d)</b> can be thought of as boron analogues of ethane (dicarbane<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>), propane (tricarbane<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>) and cyclobutane (cyclotetracarbane<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>), respectively. Logically enough, we can name <b>(b)</b> diborane, <b>(c)</b> triborane and <b>(d)</b> cyclotetraborane. Right? </p>
<p> And now the moment’s gone. Boron hydride nomenclature, in contrast to that of hydrocarbons, <i>explicitly</i> specifies the number of hydrogen atoms in the molecule [<a href="#Red_Book_1990" target="_blank" title="Red Book (1990)">1</a>—<a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>]. This is done by placing the corresponding Arabic numeral in parentheses immediately following the name<sup><a href="#Footnote_†" title="Footnote †">†</a></sup>. Thus, <b>(b)</b> will be diborane(4), <b>(c)</b> triborane(5) and <b>(d)</b> cyclotetraborane(4). The structure <b>(c)</b> could be also named <i>catena</i>-triborane(5), the descriptor <i>catena</i> emphasising that it’s a chain [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-6.2.3.2, p. 92]. As for <b>(d)</b>, the Blue Book gives the <a href="http://metallome.blogspot.com/2021/04/hantzsch-widman-names.html" target="_blank" title="Hantzsch-Widman names @ this blog">Hantzsch-Widman</a> name — back to implicit hydrogen! — ‘tetraboretane’ as preselected [<a href="#Blue_Book_2014" title="Blue Book (2014)">4</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P6a.html#6801010302" target="_blank" title="Blue Book, P-68.1.1.3.2">P-68.1.1.3.2</a>]. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33600" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="triborylborane (CHEBI:33600)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhONlZCJWa4-xDCTZRgad4gbnUQjOYCwI7CUjeM9wZmOTyiojtL78qTKeXYKYaJnLNXPs3QwcQsugzfLFUJhJG14_odvRHU8APxZr1Ze2YKPvHRl75djc2sTVG1APq6C7SgeDEShsfUtg_ipdnGZ0_mGWIIb0ViFTt8FF0x-CvABaodMhxdsVs/s1600/triborylborane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(e)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> B<sub>4</sub>H<sub>6</sub> <br />
B(BH<sub>2</sub>)<sub>3</sub> <br />
2-boranyltriborane(5) (<i>boron hydride + substitutive</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Since the name of the group –BH<sub>2</sub> is <span style="background-color: lavender;">boranyl</span>, the molecule <b>(e)</b> could be named substitutively <span style="background-color: lavender;">triboranyl</span><span style="background-color: yellow;">borane</span>. However, the IUPAC name is 2-<span style="background-color: lavender;">boranyl</span><span style="background-color: yellow;">triborane(5)</span>. Although <b>(e)</b> contains six hydrogens, the numeral in parentheses is 5. Why? Because this name is based on the parent hydride <span style="background-color: yellow;">triborane(5)</span> <b>(c)</b>, substituted by one <span style="background-color: lavender;">boranyl</span> group at the position 2.<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup></p>
<p> Why do we even have to specify the number of hydrogens? Consider the structure <b>(f)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33590" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="diborane(6) (CHEBI:33590)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjydZrknlOedc2UteSbTei84gSIk-oDxhDCEx2X_se3F-gBaLuclW7Jm-PfQig1JtKw2Tilqqb8jC263xOvajGuvGEsKmy4lF4RuDqWMtEkdAwTKAoyVvBioWvGeJ9Jt6zZUAMkCg/s0/diborane%25286%2529.png" /></a></td>
</tr>
<tr><th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="6" type="a">
<li> B<sub>2</sub>H<sub>6</sub> <br />
diborane(6) (<i>boron hydride, preselected name</i>) <br />
di-μ-hydrido-bis(dihydridoboron) (<i>additive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> It is also a ‘<a href="http://en.wikipedia.org/wiki/Diborane" target="_blank" title="Diborane in Wikipedia">diborane</a>’ and it is very different from diborane(4) <b>(b)</b>. Not only does <b>(f)</b> contain two <i>tetravalent</i> boron atoms, but it also has two bridging hydrogens. We can name it additively by analogy with other inorganic <a href="http://metallome.blogspot.com/2020/06/dinuclear-and-polynuclear-entities.html" target="_blank" title="Dealing with dinuclear and polynuclear entities @ this blog">dinuclear entities</a>: <span style="background-color: lightgreen;">di-μ-hydrido</span>-bis(<span style="background-color: lightgreen;">dihydrido</span><span style="background-color: gold;">boron</span>). However, this compound is given much shorter, albeit less descriptive, preselected name diborane(6) [<a href="#Blue_Book_2014" title="Blue Book (2014)">4</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P6a.html#6801010201" target="_blank" title="Blue Book, P-68.1.1.2.1">P-68.1.1.2.1</a>]. </p>
<p> The problem is, the composition of even simplest boranes does not tell us what their structure is. For example, the structure <b>(b)</b> is not the <i>only</i> possible diborane(4). A few years ago, its isomer <b>(g)</b> has been identified [<a href="#Chou_2015" name="Chou et al. (2015)">5</a>]: </p>
<center>
<table>
<tr>
<td><a href="http://en.wikipedia.org/wiki/Diborane(4)" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="Diborane(4) in Wikipedia"><img border="0" data-original-height="200" data-original-width="200" height="77" src="https://upload.wikimedia.org/wikipedia/commons/8/8c/Diborane4.png" width="200" /></a></td>
</tr>
<tr><th align="center">(g)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> B<sub>2</sub>H<sub>4</sub> <br />
di-μ-hydrido-bis(hydridoboron)(<i>B</i>—<i>B</i>) (<i>additive</i>) <br />
di-μ-hydrido-dihydridodiboron(<i>B</i>—<i>B</i>) (<i>additive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> To differentiate between the two isomers, we can name <b>(b)</b> substitutively <span style="background-color: lavender;">boranyl</span><span style="background-color: yellow;">borane</span> and <b>(g)</b> additively <span style="background-color: lightgreen;">di-μ-hydrido</span>-<span style="background-color: lightgreen;">dihydrido</span><span style="background-color: gold;">diboron</span>(<i>B</i>—<i>B</i>) or <span style="background-color: lightgreen;">di-μ-hydrido</span>-bis(<span style="background-color: lightgreen;">hydrido</span><span style="background-color: gold;">boron</span>)(<i>B</i>—<i>B</i>). None of these names is short or elegant but they do describe the structure. </p>
<p> Polynuclear boranes tend to form cages where boron atoms occupy vertices of closed or open triangulated polyhedra, or <a href="http://en.wikipedia.org/wiki/Deltahedron" target="_blank" title="Deltahedron in Wikipedia">deltahedra</a> [<a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>]. This means that any boron atom at a polyhedral vertex should be <i>at least</i> tetracoordinate. As you can imagine, simply indicating the composition won’t be nearly enough. <a href="http://metallome.blogspot.com/2023/04/lambda-convention.html" target="_blank" title="λ-convention @ this blog">λ-convention</a> is not of much use here either as you’ll need to add “lambdas” to all boron atoms. To make the names of boranes more informative, they have to be modified with special structural descriptors [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-6.2.3.2]: </p>
<center><table>
<tr> <th>Descriptor</th> <th>Parent hydride</th> <th>Description of structure</th> </tr>
<tr> <td><i>closo</i></td> <td>B<sub><i>n</i></sub>H<sub><i>n</i>+2</sub></td> <td> Closed deltahedral structure </td> </tr>
<tr> <td><i>nido</i></td> <td>B<sub><i>n</i></sub>H<sub><i>n</i>+4</sub></td> <td> Nest-like non-closed polyhedral structure; a deltahedron with one vertex missing </td> </tr>
<tr> <td><i>arachno</i></td> <td>B<sub><i>n</i></sub>H<sub><i>n</i>+6</sub></td> <td> Web-like non-closed polyhedral structure; a deltahedron with two vertices missing </td> </tr>
<tr> <td><i>hypho</i></td> <td>B<sub><i>n</i></sub>H<sub><i>n</i>+8</sub></td> <td> Net-like non-closed polyhedral structure; a deltahedron with three vertices missing </td> </tr>
<tr> <td><i>klado</i></td> <td>B<sub><i>n</i></sub>H<sub><i>n</i>+10</sub></td> <td> Open branch-like non-closed polyhedral structure; a deltahedron with four vertices missing </td> </tr>
</table></center>
<p> To make a connection between a descriptor, the number of boron atoms and resulting deltahedron, it could be useful to have a look-up diagram, like the one given in the recent Recommendations [<a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>, p. 358, Fig. 1]. One certainly <i>needs</i> such a diagram to work out the numbering of boron atoms in a cage. </p>
<center><p><a href="http://www.degruyter.com/document/doi/10.1515/pac-2018-0205/html#j_pac-2018-0205_s_003" target="_blank" title="Fig. 1: Conventional triangulated polyhedra with 4–12 vertices, illustrating closo framework cage geometries, and showing numbering conventions."><img border="0" height="400" src="https://www.degruyter.com/document/doi/10.1515/pac-2018-0205/asset/graphic/j_pac-2018-0205_fig_001.jpg" width="324" /></a></p></center>
<p> According to the 2019 Recommendation 4 [<a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>, p. 357], </p>
<blockquote> It is recommended that structural descriptors <i>closo</i>, <i>nido</i>, and <i>arachno</i>, as defined in the 1990 recommendations, are retained. However, the polyhedral shapes for <i>hypho</i> and <i>klado</i> are structurally difficult to visualize, and the use of these descriptors is no longer acceptable. </blockquote>
<p> So... they took two descriptors away without suggesting any substitute. I don’t know how it is helpful for (re)naming formerly <i>hypho</i>- and <i>klado</i>-boranes. </p>
<p> Let’s focus on the remaining three descriptors. For example, the <i>closo</i> structure <b>(h)</b> is an octahedral cage with all vertices occupied by boron atoms. Taking away one boron atom (and adding the appropriate number of hydrogens) brings about the <i>nido</i> structure <b>(i)</b>; taking away one more yields the <i>arachno</i> structure <b>(j)</b>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33593" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="hexahydro-closo-hexaborate(2−) (CHEBI:33593)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgI57iVCVObHwbWtDqpk9_DzMhXcYJ167UFVdgotMFQTpjXE8b4lYH1NYYCKzRguKyy6amFP6WcwTK0Wk1fUTKS0pJAlRnj8JrRYH3H_PsRmiRKiYR_gLSJxD7sbkce7xVqw6jVWlZfs_69h626LOu7T_aGN0WvzTn3YrNi3ZCVI0JnLLnAlq4/s1600/B6H6.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33591" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="pentaborane(9) (CHEBI:33591)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZLNbcS_a-P2WOET4hScrhRpZxYIwwcajj4vfXVZV202NAiTb6c6Gh_LM_AyJNsxhN8kNiqhjIPzCpkvurPVJ5suYWY4-2ubzHaMAOaNx-7MC6-tEi24EB_Cu4sdMspvHmGraAO9egD93o2ofKNnBf4wHrsjsG9iIj5wseimKCsIdtwTnJoE0/s1600/pentaborane(9).png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33592" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tetraborane(10) (CHEBI:33592)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBGKgWd51e_Jp2AZfbKSB8ZEGkyMHhlHnCeUL4cWyq6wOy4iNjnmJqjKuKV8aIlgkicmtvlBB5eEo0AabBhk8Yobcst_u-YK-itobESmJ3MjsyPBAt5uAAtfSp8Aucdt68o7jwq60ygiphPOJKHCkEc6PtHmYyJYQaSdgYu1ABK22pQFoV3L4/s1600/tetraborane(10).png" width="200" /></a></td>
</tr>
<tr><th align="center">(h)</th> <th align="center">(i)</th> <th align="center">(j)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="8" type="a">
<li> [B<sub>6</sub>H<sub>6</sub>]<sup>2−</sup> <br />
hexahydrido-<i>closo</i>-hexaborate(2−) (<i>boron hydride</i>) </li>
<li> B<sub>5</sub>H<sub>9</sub> <br />
<i>nido</i>-pentaborane(9) (<i>boron hydride, preselected name</i>) </li>
<li> B<sub>4</sub>H<sub>10</sub> <br />
<i>arachno</i>-tetraborane(10) (<i>boron hydride, preselected name</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The name of the anionic boron hydride <b>(h)</b> is strikingly different from those of neutral boranes such as <b>(i)</b> and <b>(j)</b>. Note it does not contain ‘(6)’; instead, the hydrogens in <i>hydridoborates</i> are indicated in a familiar additive way (that is, ligands first): <span style="background-color: lightgreen;">hexahydrido</span>-<span style="background-color: gold;"><i>closo</i>-hexaborate</span>(2−). Maybe this is because the parentheses are needed now to accommodate the charge? </p>
<p> Boron atoms in polyboranes could be replaced by atoms of other elements, resulting in <i>heteroboranes</i>. They are named using <a href="http://metallome.blogspot.com/2020/06/skeletal-replacement-nomenclature.html" target="_blank" title="Skeletal replacement nomenclature @ this blog">skeletal replacement</a> (aka ‘a’) nomenclature. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:38277" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="closo-dodecaborane(12) (CHEBI:38277)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFNt0FGwzRw8AUOOuP1xfdVuAui8qPO4wtQ3vszt139m_tbHkZGbxIESwo__mufOMKnP-rZEh_Hm1Bzx9mLqcttRzsnetOZ0ltw82S1TwE2qVtsRV-sEmkFZ62bl15hiDFuEzepg/s1600/closo-dodecaborane%252812%2529.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:38283" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,2-dicarba-closo-dodecaborane(12) (CHEBI:38283)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihrXGFWcwHoBLjWhfoi0PEfsi0Us-jxwI1RHt7zSAoOdlzqHzFGHJMjwxS5z7Q-ff5KvaWvYsbhiu8t5t-pf6Sxg-VnvM2XhGbXPEzbNoNHVRliEIuU6ao2pwSvpKwwHHVL_OID7CEKCV4so8NCnNJnPFh9eCOSsdFJ6tlsRUg6kQNwLdkpTc/s1600/1,2-dicarba-closo-dodecaborane(12).png" width="200" /></a></td></tr>
<tr><th align="center">(k)</th> <th align="center">(l)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="11" type="a">
<li> B<sub>12</sub>H<sub>12</sub> <br />
<i>closo</i>-dodecaborane(12) </li>
<li> B<sub>10</sub>C<sub>2</sub>H<sub>12</sub> <br />
<i>closo</i>-1,2-dicarbadodecaborane(12) (<i>replacement</i>) </li>
</ol>
</td></tr>
</table>
</center>
<p> For example, replacing two boron atoms with carbons in <span style="background-color: yellow;"><i>closo</i>-dodecaborane(12)</span> <b>(k)</b> begets <span style="background-color: yellow;"><i>closo</i></span>-1,2-<span style="background-color: paleturquoise;">dicarba</span><span style="background-color: yellow;">dodecaborane(12)</span> <b>(l)</b>. Carbon-replaced boranes are commonly known as <a href="http://en.wikipedia.org/wiki/Carborane" target="_blank" title="Carborane in Wikipedia"><i>carboranes</i></a>, another deprecation victim of the Recommendations [<a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>].
</p>
<p> Skeletal replacement in boranes is called <a href="http://en.wiktionary.org/wiki/subrogation" target="_blank" title="subrogation in Wiktionary"><i>subrogation</i></a> [<a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>, BN-4.2]. It’s a mystery how — and why — this atrocious <a href="http://en.wikipedia.org/wiki/Subrogation" target="_blank" title="Subrogation in Wikipedia">legalese term</a> and a host of its relatives (subrogate, subrogating, subrogated, unsubrogated) have found its way into IUPAC recommendations. </p>
<p> To sum up: borane nomenclature is an uneasy hybrid of pseudo-organic (parent hydride-based) and inorganic additive naming systems, with some specific features such as hydrogens in parentheses and <i>closo</i>/<i>nido</i>/<i>arachno</i> descriptors thrown in. It works and parts of it are “well entrenched in the <boron hydride related> literature” [<a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>]; outside of the field, it’s bound to keep unhappy both inorganic and organic chemists. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> The systematic name ‘carbane’ is not recommended by IUPAC “because of the universal use of the name ‘methane’” [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, p. 85, Table IR-6.1]. </td></tr>
<tr><td valign="top">†</td>
<td> The IUPAC Recommendations [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-6.2.3.1; <a href="#Beckett_2020" title="Beckett et al. (2020)">3</a>] employ the terms <i>stoichiometric names</i> or <i>compositional names</i> for constructs <i>à la</i> ‘diborane(4)’, which is confusing given that elsewhere [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, IR-5.2] “stoichiometric names” refer to the likes of ‘diboron tetrahydride’. </td></tr>
<tr><td valign="top">‡</td>
<td> You may recall a similar situation with <a href="http://metallome.blogspot.com/2021/02/branched-hydrocarbons.html#neopentane" target="_blank" title="Branched hydrocarbons @ this blog">neopentane</a> where a longest chain-based name ‘2,2-dimethylpropane’ is preferred to a perfectly symmetrical ‘tetramethylmethane’. </td>
</tr>
</table>
<h4>References</h4>
<ol>
<a name="Red_Book_1990"></a>
<li> Leigh, G.J. (ed.) <i>Nomenclature of Inorganic Chemistry, Recommendations 1990</i>. Blackwell Science, 1990. </li>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
<a name="Beckett_2020"></a>
<li> Beckett, M.A., Brellochs, B., Chizhevsky, I.T., Damhus, T., Hellwich, K.-H., Kennedy, J.D., Laitinen, R., Powell, W.H., Rabinovich, D., Viñas, C. and Yerin, A. (2020) Nomenclature for boranes and related species (IUPAC Recommendations 2019). <a href="http://doi.org/10.1515/pac-2018-0205" target="_blank" title="Pure Appl. Chem. 92, 355-381."><i>Pure and Applied Chemistry</i> <b>92</b>, 355—381</a>. </li>
<a name="Blue_Book_2014"></a>
<li><a name="Blue_Book_2014"> Favre, H.A. and Powell, W.H. </a><a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
<a name="Chou_2015"></a>
<li> Chou, S.-L., Lo, J.-I., Peng, Y.-C., Lin, M.-Y., Lu, H.-C., Cheng, B.-M. and Ogilvie, J.F. (2015) Identification of diborane(4) with bridging B–H–B bonds. <a href="http://doi.org/10.1039/c5sc02586a" target="_blank" title="Chem. Sci. 6, 6872-6877."><i>Chemical Science</i> <b>6</b>, 6872—6877</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-18557012547929415712023-04-01T23:00:00.042+01:002023-08-06T20:51:06.380+01:00λ-convention<p> The whole edifice of <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">substitutive nomenclature</a> is based on concept of parent structures, most importantly parent hydrides. Implicit in parent hydrides are the valencies, or <a href="http://goldbook.iupac.org/terms/view/B00703" target="_blank" title="bonding number in Gold Book">bonding numbers</a>, of non-hydrogen atoms. The standard bonding numbers of neutral atoms in parent hydrides are given thus [<a href="#Powell_1984" title="Powell (1984)">1</a>]: </p>
<center>
<table width="50%">
<tr valign="bottom"> <th>Bonding number <i>n</i></th> <th>3<sup><a href="#Footnote_*" title="Footnote *">*</a></sup></th> <th>4</th> <th>3</th> <th>2</th> <th>1</th> </tr>
<tr> <td></td> <td align="center">B</td> <td align="center">C</td> <td align="center">N</td> <td align="center">O</td> <td align="center">F</td> </tr>
<tr> <td></td> <td align="center">Al</td> <td align="center">Si</td> <td align="center">P</td> <td align="center">S</td> <td align="center">Cl</td> </tr>
<tr> <td></td> <td align="center">Ga</td> <td align="center">Ge</td> <td align="center">As</td> <td align="center">Se</td> <td align="center">Br</td> </tr>
<tr> <td></td> <td align="center">In</td> <td align="center">Sn</td> <td align="center">Sb</td> <td align="center">Te</td> <td align="center">I</td> </tr>
<tr> <td></td> <td align="center">Tl</td> <td align="center">Pb</td> <td align="center">Bi</td> <td align="center">Po</td> <td align="center">At</td> </tr>
</table>
</center>
<p> These bonding numbers correspond to the number of hydrogen atoms in <a href="http://metallome.blogspot.com/p/parent-names-of-mononuclear-hydrides.html" target="_blank" title="Parent names of mononuclear hydrides @ this blog">mononuclear hydrides</a> for elements of Group 13 to Group 17. </p>
<p> Ah, if we only had to name compounds containing just carbon, hydrogen and oxygen. As soon as we move beyond, the trouble starts. Consider phosphorus. We know from school chemistry that this element has valencies of 3 and 5. For trivalent phosphorus compounds we can create substitutive names based on the parent hydride PH<sub>3</sub>, phosphane <b>(a)</b>. But how to deal with pentavalent phosphorus? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30278" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="phosphane (CHEBI:30278)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDlxPcWdeTEXSa8y0ciGmkP7AiYE6LbiOxWwS8-gFTf1q9CH0MoRFwj_2okcjDfpfa5LG-qTGWF18zDqNK7htvcy7YPhaS4PrEUGPJnw8kppGxsvsUSWOF7-hjC395lNYzQR9b65L4IyHWXyDvQ6VOlskXrEnXee8j_hsNfa59Hk3BYJiKQCg/w200-h200/phosphane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30285" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="phosphorane (CHEBI:30285)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh8_2k04tIBrhjdHhx4qEQxgdCv2tZ4dhDrgZgfq5cy9Fjfp7CW-LypOqW4wSswCgt0nyOfIPYnULXLQnxyLygBoCr5A1HK7bGPmriE7Gyx3DFSu1wKezgnrRimFSiVI-RugQNvCJAv2NGpkjoJ6kCocZDpwYBLL9Z2CzbWGOLIUsRTvg_dfOU/w200-h200/phosphorane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th>
</tr>
</table>
</center>
<a name='more'></a>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> phosphane (<i>preselected</i>) <br />
phosphine (<i>retained</i>) </li>
<li> λ<sup>5</sup>-phosphane (<i>preselected</i>) <br />
phosphorane (<i>retained</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Well, one can create yet another parent hydride name where bonding number differs from standard. For example, the (hypothetical) molecule PH<sub>5</sub> <b>(b)</b> is known as phosphorane. This does not seem to be such a great idea though as there’s a lot of elements that have variable valencies. According to the Blue Book [<a href="#Blue_Book_2014" title="Blue Book (2014)">2</a>, <a href="http://iupac.qmul.ac.uk/BlueBook/P2.html#21010201" target="_blank" title="Blue Book chapter P-2">P-21.1.2.1</a>], </p>
<blockquote> The names ‘phosphorane’ for PH<sub>5</sub>, ‘arsorane’ for AsH<sub>5</sub>, and ‘stiborane’ for SbH<sub>5</sub>, are retained for use in general nomenclature. However, the names ‘sulfurane’ for SH<sub>4</sub>, ‘selenurane’ for SeH<sub>4</sub>, ‘iodinane’ for IH<sub>3</sub>, ‘persulfurane’ for SH<sub>6</sub>, and ‘periodinane’ for IH<sub>5</sub>, which have been used in recent literature, are not recommended. </blockquote>
<p> More general approach, known as “lambda convention”<sup><a href="#Footnote_†" title="Footnote †">†</a></sup>, is to modify the existing name of the hydride with the symbol λ<sup><i>n</i></sup>, where ‘<i>n</i>’ is the bonding number [<a href="#Powell_1984" title="Powell (1984)">1</a>]. So the structure <b>(b)</b> is named λ<sup>5</sup>-phosphane. </p>
<p> Now let’s have a look at some organic molecules. Consider the stucture <b>(c)</b>. As its <a href="http://metallome.blogspot.com/2020/09/additive-again.html" target="_blank" title="Additive again @ this blog">additive name</a>, <span style="background-color: gold;">benzonitrile</span> <span style="background-color: lightgreen;">oxide</span>, suggests, it is a derivative of <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27991" target="_blank" title="benzonitrile (CHEBI:27991)">benzonitrile</a>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37829" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="benzonitrile oxide (CHEBI:37829)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0fHJTHjVBaqqRC2cnqooWuYo2dy6lhUEmTzcmahhtyLm56jMHaQJSJevgczL14BXEbtIfy65Q8xMNG2olG1C5owtEZ6KcKSSYN5GiUApf5mRRQCTQ0owSbRfGS-O6NOf_gRW_UaStzpUHH4Lno1UKoqqazd4vYYl8yz564n-uXbj6O6ojRVw/w200-h200/benzonitrile_oxide.png" width="200" /></a></td>
</tr>
<tr><th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="3" type="a">
<li> benzonitrile oxide (<i>substitutive + <a href="http://metallome.blogspot.com/2020/09/additive-again.html" target="_blank" title="Additive again @ this blog">additive</a></i>) <br />
(benzylidyneammoniumyl)oxidanide (<i>substitutive</i>) <br />
benzylidyne(oxo)-λ<sup>5</sup>-azane (<i>substitutive</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Can we name it using purely substitutive nomenclature? Yes we can, using oxidane as parent hydride, but the resulting name, (<span style="background-color: lavender;">benzylidyneammoniumyl</span>)<span style="background-color: yellow;">oxidanide</span>, is rather cumbersome. And it is not just its length. Here, <span style="background-color: lavender;">benzylidyne</span>, <span style="background-color: lavender;">ammoniumyl</span> and <span style="background-color: yellow;">oxidanide</span> refer to the <span style="background-color: lavender;">≡CPh</span> group, <span style="background-color: lavender;">–N<sup>+</sup>≡</span> group, and <span style="background-color: yellow;">HO<sup>−</sup></span> anion, respectively. So the whole name sounds as that of an anion, while <b>(c)</b> is a neutral molecule. One can argue that it simply reflects the way the structure <b>(c)</b> is drawn. </p>
<p> Very well. Let’s redraw the structure in such a way that the charges disappear<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37829" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="benzonitrile oxide (CHEBI:37829)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgg8aa8fjDq6TNO2wzIiqL_kkEu34JfX95EeNY3NIPjXMxgtWDAdF-dMyovnvvDvEE40Q1IGXuJQ6h3prlQBRyByyYBLTm7A4zYXgQdDR1XFe11HQIuZLJ3LrZ2YsTHxVD7qPrTUCMC_ClBgPM1vYKja0768sJnL8Cq9cZqqomTv-xhnSSev7w/w200-h200/benzonitrile_oxide.png" width="200" /></a></td>
</tr>
<tr><th align="center">(c′)</th>
</tr>
</table>
</center>
<p> By applying λ-convention, we can come with a different substitutive name, viz. <span style="background-color: lavender;">benzylidyne</span>(<span style="background-color: lavender;">oxo</span>)-<span style="background-color: yellow;">λ<sup>5</sup>-azane</span>, where <span style="background-color: lavender;">benzylidyne</span>, <span style="background-color: lavender;">oxo</span> and <span style="background-color: yellow;">λ<sup>5</sup>-azane</span> correspond to the <span style="background-color: lavender;">≡CPh</span> group, <span style="background-color: lavender;">=O</span> group, and hypothetical <span style="background-color: yellow;">NH<sub>5</sub></span> parent hydride, respectively. </p>
<p> The same principle applies to heterocycles containing heteroatoms with nonstandard bonding numbers: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36603" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="thiophene oxide (CHEBI:36603)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyVG3SeptC54t5T2Lqfa4Kl0P_fVnofVc_3kRBCICoiadeyiU_3Kvop5FfIz7ggqMaGLi6aI02gD85TWEnHItW-MuOlJqgtPw3U60nfeFqBNVnXu4VabU_NagA4ef4bf5PhD6kf7L90THswxaHjqfGIt7sn0kCSvu64D5ZXfI1ZNVkrkA4LV4/w200-h200/thiophene_oxide.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:52701" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1-hydroxy-1,3-dioxobenziodoxole (CHEBI:52701)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjOboDOwjfTw6TQVbXlfzU9ZTUBJ74Xs8sBrjy8cQQ94pz4Bcc7rr1KRQ3cqh9PaOEMy68_wx3oCVpVmyhaYAh_8bo7CC1hyJQLgXX3oq4ASRO6feuyHhLW8WvMqPnN-FKgU8TWtajB8PswjRYJveAE_SL8q4oiw4k5__zI_ivkXnkgI5lWzOc/w200-h200/1-hydroxy-1,3-dioxobenziodoxole.png" width="200" /></a></td>
</tr>
<tr><th align="center">(d)</th> <th align="center">(e)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="4" type="a">
<li> thiophene 1-oxide (<i>additive</i>) <br />
1<i>H</i>-λ<sup>4</sup>-thiophen-1-one (<i>substitutive, <a href="http://en.wikipedia.org/wiki/Preferred_IUPAC_name" target="_blank" title="Preferred IUPAC name in Wikipedia">PIN</a></i>) <br />
1-oxo-1<i>H</i>-1λ4-thiophene (<i>substitutive</i>) </li>
<li> 1-hydroxy-1λ<sup>3</sup>,2-benziodoxol-3(1<i>H</i>)-one 1-oxide (<i><a href="http://metallome.blogspot.com/2021/04/hantzsch-widman-names.html" target="_blank" title="Hantzsch-Widman names @ this blog"><i>Hantzsch-Widman</i></a> + <a href="http://metallome.blogspot.com/2021/05/fused-ring-names.html" target="_blank" title="Fused ring names @ this blog">fused ring</a> + substitutive + additive</i>) <br />
1-hydroxy-1-oxo-1λ<sup>5</sup>,2-benziodoxol-3-one (<i>H-W + fused ring + substitutive</i>) <br />
1-hydroxy-1λ<sup>5</sup>,2-benziodoxole-1,3-dione (<i>H-W + fused ring + substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> For the structure <b>(d)</b>, I prefer the additive name, thiophene oxide, to the unwieldy 1<i>H</i>-λ<sup>4</sup>-thiophen-1-one, just because the former is shorter. On the other hand, for the structure <b>(e)</b> I would avoid 1-hydroxy-1λ<sup>3</sup>,2-benziodoxol-3(1<i>H</i>)-one 1-oxide because it mixes substitutive and additive nomenclatures: one =O group is named ‘one’ and another ‘oxide’. On top of that, λ<sup>3</sup> descriptor for clearly pentavalent iodine looks weird. Similarly, in a substitutive name 1-hydroxy-1-oxo-1λ<sup>5</sup>,2-benziodoxol-3-one the first =O group is ‘oxo’ and another ‘one’. The name 1-hydroxy-1λ<sup>5</sup>,2-benziodoxole-1,3-dione is the most compact (and logical) one. </p>
<p> Simetimes the introduction of λ<sup><i>n</i></sup> descriptors may look like an unnecessary trick. For instance, 1,3,5,2,4,6-triazatriphosphinine <b>(f)</b> cannot be considered a parent hydride of apholate <b>(g)</b> for a simple reason that <b>(f)</b> does not have any hydrogen atoms. Solution? A pair of hydrogens is added to each phosphorus atom to generate a parent hydride, 1,3,5,2λ<sup>5</sup>,4λ<sup>5</sup>,6λ<sup>5</sup>-triazatriphosphinine, only to be taken away when substituted by aziridinyl groups, giving 2,2,4,4,6,6-hexakis(aziridin-1-yl)-1,3,5,2λ<sup>5</sup>,4λ<sup>5</sup>,6λ<sup>5</sup>-triazatriphosphinine. Dropping those unpronounceable “lambdas” from that name won’t result in any ambiguity: 2,2,4,4,6,6-hexakis(aziridin-1-yl)-1,3,5,2,4,6-triazatriphosphinine is a name that a coordination chemist would come up with anyway. Still a mouthful, but every little helps. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:167642" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3,5,2,4,6-triazatriphosphinine (CHEBI:167642)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQ_OIwBiKHFgNmB9A1TWAhdynToxw8KMZAzSs77L-XQHs2Kae1QoN8-1ynD0h5o3Au1fLY48PyW5QgEoBvoMrqLOxH5FE7XWVDEeq4Akz5O7cS6HY7aTqMEDP3DH2xKWab5aXigrUvop1JTE1bVYUrLMyMzQCJD4GPkIXOVx1tl41ZZvwjluY/w200-h200/cyclotriphosphazene.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33111" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="apholate (CHEBI:33111)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWYzYhYWXCZmiYCc_yQxvRyxDlchRt2kLICACl2A662O-4tv5MM4kJagfv1-N6lFQzzH_9OZ3UYqF1_-v5aD6Qzp26RQkB1TvCjdcO1PUs1L-ppPg1ShLtLWvM5FSXYVXn5dRWNA/w200-h200/apholate.png" width="200" /></a></td>
</tr>
<tr><th align="center">(f)</th> <th align="center">(g)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="6" type="a">
<li> 1,3,5,2,4,6-triazatriphosphinine (<i>H-W</i>) <br />
1,3,5-triaza-2,4,6-triphosphacyclohexa-1,3,5-triene (<i>replacement</i>) </li>
<li> apholate (<i>trivial</i>) <br />
2,2,4,4,6,6-hexakis(aziridin-1-yl)-1,3,5,2λ<sup>5</sup>,4λ<sup>5</sup>,6λ<sup>5</sup>-triazatriphosphinine (<i>H-W + substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> In the original publication on lambda convention [<a href="#Powell_1984" title="Powell (1984)">1</a>, <a href="http://iupac.qmul.ac.uk/hetero/Lm1t4.html#lm12" target="_blank" title="Lambda Convention Recommendations, Lm-1.2: Standard Bonding Number">Lm-1.2</a>], the standard bonding number ‘3’ was given to boron but not to the rest of Group 13; I allowed myself to complete the table. </td></tr>
<tr><td valign="top">†</td>
<td> It was never explained in the original publication [<a href="#Powell_1984" title="Powell (1984)">1</a>] why the Greek letter λ (<a href="http://justsomesymbols.blogspot.com/2017/05/lambda.html" target="_blank" title="λ | lambda @ just some symbols">lambda</a>) was chosen. </td></tr>
<tr><td valign="top">‡</td>
<td> Whether one could (or should) draw pentavalent nitrogen was discussed years ago on this blog in relation to <a href="http://metallome.blogspot.com/2009/04/how-to-draw-nitro-group.html" target="_blank" title="How to draw a nitro group @ this blog">nitro group</a>. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Powell_1984"></a>
<li> Powell, W.H. (1984) Treatment of variable valence in organic nomenclature (lambda convention) (Recommendations 1983). <a href="http://doi.org/10.1351/pac198456060769" target="_blank" title="Powell (1984) Pure Appl. Chem. 56, 769-778."><i>Pure and Applied Chemistry</i> <b>56</b>, 769—778</a>. </li>
<a name="Blue_Book_2014"></a>
<li> Favre, H.A. and Powell, W.H. <a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-13720068581593705162022-01-23T15:00:00.033+00:002023-08-06T20:55:46.656+01:00Inorganic chains and rings<p> Let’s name a simple inorganic chain <b>(a)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29804" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,2-dinitrosodioxidane (CHEBI:29804)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEiRm6bs88FL8opdUHlNjfaarAmC4xKDfXwfO869ZWAu57dqDVnbdh7IViq76PBw82XFsvLyULzd-zyqkm59uzXMF71_Bu8jhKdBsLPrdghj7KEnVzEj1Pni3kfIBFmkBwVsK0Jz6g0pNVzPi29o-x5yrEEf25i2SWPRZUWbsi0uK5o40eivExw=w200-h200" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="1" type="a">
<li> 1,2-dinitrosodioxidane (<i>substitutive</i>) <br />
bis(nitrosyloxygen)(<i>O</i>—<i>O</i>) (<i>additive</i>) <br />
2,5-diazy-1,3,4,6-tetraoxy-[6]catena (<i>ICR</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> The shortest systematic name I can think about is 1,2-<span style="background-color: lavender;">dinitroso</span><span style="background-color: yellow;">dioxidane</span>, based on the <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">parent hydride</a> <span style="background-color: yellow;">dioxidane</span> (aka <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16240" target="_blank" title="hydrogen peroxide (CHEBI:16240)">hydrogen peroxide</a>). Alternatively, we can emphasise the structure’s symmetry by naming it as a <a href="http://metallome.blogspot.com/2020/06/dinuclear-and-polynuclear-entities.html" target="_blank" title="Dealing with dinuclear and polynuclear entities @ this blog">dinuclear entity</a>, bis(<span style="background-color: lightgreen;">nitrosyl</span><span style="background-color: gold;">oxygen</span>)(<i>O</i>—<i>O</i>). </p>
<p> Or we can have a go at it employng yet <i>another</i> type of nomenclature developed for inorganic chains and rings (ICR): 2,5-diazy-1,3,4,6-tetraoxy-[6]catena [<a href="#Fluck_and_Laitinen_1997" title="Fluck & Laitinen (1997)">1</a>, <a href="#Red_Book_2005" title="Red Book (2005)">2</a> IR-7.4]. What’s going on here? </p>
<a name='more'></a>
<p> The ‘catena’ bit means that the structure in question is a chain; ‘[6]catena’ simply says that the chain consists of six atoms:</p>
<center><table>
<tr><td align="center">X<sub>1</sub>–X<sub>2</sub>–X<sub>3</sub>–X<sub>4</sub>–X<sub>5</sub>–X<sub>6</sub></td></tr>
</table></center>
<p> All atoms in the chain are named with ‘y’ terms [<a href="#Fluck_and_Laitinen_1997" title="Fluck & Laitinen (1997)">1</a>, Table 1], in our case ‘<span style="background-color: gold;">azy</span>’ for nitrogen and ‘<span style="background-color: gold;">oxy</span>’ for oxygen, and listed alphabetically. They are preceded by corresponding Greek-derived multipliers, thus ‘<span style="background-color: gold;">diazy</span>’ and ‘<span style="background-color: gold;">tetraoxy</span>’. The locants indicate the positions of each type of atom in the chain, so ‘2,5-<span style="background-color: gold;">diazy</span>’ and ‘1,3,4,6-<span style="background-color: gold;">tetraoxy</span>’. </p>
<center><table>
<tr><td align="center">O<sub>1</sub>–N<sub>2</sub>–O<sub>3</sub>–O<sub>4</sub>–N<sub>5</sub>–O<sub>6</sub></td></tr>
</table></center>
<p> The resulting name, 2,5-<span style="background-color: gold;">diazy</span>-1,3,4,6-<span style="background-color: gold;">tetraoxy</span>-[6]catena, is as straightforward as it is boring. To interpret it, you don’t need to know the names of parent hydrides (such as <span style="background-color: yellow;">dioxidane</span>), groups (like <span style="background-color: lavender;">nitroso</span>) or ligands (<span style="background-color: lightgreen;">nitrosyl</span>). Still, one might wonder if it’s worth the bother to create such a long name for ONOONO. </p>
<p> We can name ring structures in a similar fashion, except for using ‘cycle’ instead of ‘catena’. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37756" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="disulfur dinitride (CHEBI:37756)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEjQNUD29TS4mlIqAjPpKsHWYr93UQIrKwdUoxog_rdyKpzYDxYGz9gp8z_1l4HNI8ZJ8qo_E5ummf3ClKUayBwveJbB2ePUgCOZgWKCEDwr8tcU294cLD-dj906J5AjkI42SMYfgDa_9LAISaLZ54t1FGz2oP_GWKHxNhwmwFDvtsEL3A46IuA=w200-h200" width="200" /></a></td>
</tr>
<tr><th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="2" type="a">
<li> disulfur dinitride (<i>binary-type</i>) <br />
1λ<sup>4</sup>,3-dithia-2,4-diazacyclobuta-1,4-diene (<i>replacement</i>) <br />
1λ<sup>4</sup>,3,2,4-dithiadiazete (<i>H-W</i>) <br />
2,4-diazy-1,3-disulfy-[4]cycle (<i>ICR</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> For instance, the structure <b>(b)</b> will be 2,4-<span style="background-color: gold;">diazy</span>-1,3-<span style="background-color: gold;">disulfy</span>-[4]cycle. This name requires minimal <i>a priori</i> knowledge (just that of ‘y’ terms) while describing exactly what <b>(b)</b> is. In contrast, the name like 1λ<sup>4</sup>,3,2,4-dithiadiazete calls for familiarity with <a href="http://metallome.blogspot.com/2021/04/hantzsch-widman-names.html" target="_blank" title="Hantzsch-Widman names @ this blog">Hantzsch-Widman nomenclature</a> as well as <a href="http://metallome.blogspot.com/2023/04/lambda-convention.html" target="_blank" title="λ-convention @ this blog">λ-convention</a> [<a href="#Powell_1984" title="Powell (1984)">3</a>], while the binary-type name, <span style="background-color: lightpink;">disulfur</span> <span style="background-color: lightblue;">dinitride</span>, does not even tell us that <b>(b)</b> is a ring.
</p>
<p> So far so good. To quote the Red Book [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, p. 118], </p>
<blockquote> the advantage of this nomenclature system lies in the simplicity with which complicated structures can be derived from the name and <i>vice versa</i>. </blockquote>
<p> What if chains or rings have groups/ligands attached? Then they can be named as, well, groups or ligands [<a href="#Fluck_and_Laitinen_1997" title="Fluck & Laitinen (1997)">1</a>, p. 1681]: </p>
<blockquote> In principle all atoms in the molecule can be treated as a part of the nodal framework. The resulting names will, however, become too cumbersome to be practical. Therefore it is preferable to name some atoms or groups of atoms as ligands to the nodal skeleton. </blockquote>
<p> Consider triphosphoric acid <b>(c)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:39949" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="triphosphoric acid (CHEBI:39949)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEjRGJYbMVn7JbpQIe_K_XI7eTrpIvshWEYDXh4jF9eCfHVmhEZEINgjC0Vy7zQaiTg-DCgUGiLqHROI-qSvSiiBLkPhRbMnNXn26Cqs2cJjIKZBPcUlzVBLr0pwPysWbq3ECMnuzhgGZfoN0cPLZ3LitSsSOoY-Y0Fik8DO9sp90ZEpQmabnFs=w200-h200" width="200" /></a></td>
</tr>
<tr><th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="3" type="a">
<li> triphosphoric acid (<i>trivial</i>) <br />
<i>catena</i>-triphosphoric acid (<i>trivial</i>) <br />
bis(dihydroxidodioxidophosphato)hydroxidooxidophosphorus (<i>additive</i>) <br />
μ-(hydroxidotrioxido-1κ<i>O</i>,2κ<i>O</i>′-phosphato)-bis(dihydroxidooxidophosphorus) (<i>additive</i>) <br />
1,7-dihydrido-2,4,6-trihydroxido-2,4,6-trioxido-1,3,5,7-tetraoxy-2,4,6-triphosphy-[7]catena (<i>ICR</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Its “practical” ICR name will be 1,7-<span style="background-color: lightgreen;">dihydrido</span>-2,4,6-<span style="background-color: lightgreen;">trihydroxido</span>-2,4,6-<span style="background-color: lightgreen;">trioxido</span>-1,3,5,7-<span style="background-color: gold;">tetraoxy</span>-2,4,6-<span style="background-color: gold;">triphosphy</span>-[7]catena [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, p. 134]. As you can see, it is a combination of a chain named in a “pure” ICR fashion with standard <a href="http://metallome.blogspot.com/2020/06/addictive-names.html" target="_blank" title="Addi(c)tive names @ this blog">additive nomenclature</a> for ligands<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16517" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclotriphosphoric acid (CHEBI:16517)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEgFB7f69XQY1-vHkWxi9IU0ridHB2zEuBvinZR4ZGBjR-kKV4YgeVaCCmKGqwE5yc_r8Gx1kkIJaMUqAu0xxCwAjhOWX9GikDScprWgC1pGpVfXGLXNXOymg1iSszjoFgWU_tKp9qYt0JHC-zGFo6LywAhcSCSBkTlmHIOYN08O9RQAVcFRmEQ=w200-h200" width="200" /></a></td>
</tr>
<tr><th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="4" type="a">
<li> trimetaphosphoric acid (<i>trivial</i>) <br />
<i>cyclo</i>-triphosphoric acid (<i>trivial</i>)<br />
tri-μ-oxido-tris(hydroxidooxidophosphorus) (<i>additive</i>) <br />
1,3,5,2,4,6-trioxatriphosphinane-2,4,6-triol 2,4,6-trioxide (<i>H-W</i>) <br />
2,4,6-trihydroxido-2,4,6-trioxido-1,3,5-trioxy-2,4,6-triphosphy-[6]cycle (<i>ICR</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Likewise, the ICR name for <b>(d)</b> will be 2,4,6-<span style="background-color: lightgreen;">trihydroxido</span>-2,4,6-<span style="background-color: lightgreen;">trioxido</span>-1,3,5-<span style="background-color: gold;">trioxy</span>-2,4,6-<span style="background-color: gold;">triphosphy</span>-[6]cycle [<a href="#Red_Book_2005" title="Red Book (2005)">2</a>, p. 133]. </p>
<p> Now I don’t know about you but I find the whole ligand-attaching business disappointing; this is how the hope of simplicity begins to fade. But wait, you ain’t seen nothing yet. </p>
<p> Examples <b>(a)</b>—<b>(d)</b> show simple chains and rings. Imagine that you need to name the structures that contain branched chains, or more than one ring, or combinations thereof. The overall topology of the structure is specified by combining ‘catena’ and/or ‘cycle’ with Greek multipliers ‘di’, ‘tri’, etc., as in ‘dicatena’, ‘tricycle’, ‘catenadicycle’ and so on. The connectivity of chains or rings is
indicated by a <i>nodal descriptor</i>, which looks like a bridge descriptor in <a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog">von Baeyer nomenclature</a>. Except it isn’t. Observe the structure <b>(e)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:144345" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tris(trimethylsilyl) phosphate (CHEBI:144345)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEgFgkKarZ5k0vLxqN0QvAJJ4pVLjuN8iqKkkldVpsAU69hh1QJ8enxCuo0U3CE8M1kfbQlVFfVNiSEmVWc-ywRka3T_m_5DxFaQVW3HJktCwTy-bEgfr50-wpqzml-UA86fh9VrsXaOo3go3TYzDs20lbluaGc1miZqX0D-CAT_8cFxAKCq8vM=w200-h200" width="200" /></a></td>
</tr>
<tr><th align="center">(e)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="5" type="a">
<li> tris(trimethylsilyl) phosphate (<i>functional class + substitutive</i>) <br />1,1,1,5,5,5,7,7,7-nonamethyl-3-oxido-2,4,6-trioxy-3-phosphy-1,5,7-trisily-[5.2<sup>3</sup>]dicatena (<i>ICR</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> It could be thought of as a branched chain consisting of two inorganic chains, thus ‘dicatena’. The main chain Si<sub>1</sub>–O<sub>2</sub>–P<sub>3</sub>–O<sub>4</sub>–Si<sub>5</sub> contains five nodes while the branch –O<sub>6</sub>–Si<sub>7</sub> has two nodes and is attached at the position 3; this is reflected in the nodal descriptor ‘[5.2<sup>3</sup>]’. Assigning the atom identities to the nodes, we get ‘2,4,6-<span style="background-color: gold;">trioxy</span>-3-<span style="background-color: gold;">phosphy</span>-1,5,7-<span style="background-color: gold;">trisily</span>-[5.2<sup>3</sup>]dicatena’. Finally, attaching the ligands ‘<span style="background-color: lightgreen;">methyl</span>’<sup><a href="#Footnote_†" title="Footnote †">†</a></sup> and ‘<span style="background-color: lightgreen;">oxido</span>’ results in 1,1,1,5,5,5,7,7,7-<span style="background-color: lightgreen;">nonamethyl</span>-3-<span style="background-color: lightgreen;">oxido</span>-2,4,6-<span style="background-color: gold;">trioxy</span>-3-<span style="background-color: gold;">phosphy</span>-1,5,7-<span style="background-color: gold;">trisily</span>-[5.2<sup>3</sup>]dicatena. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35895" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tetraphosphorus (CHEBI:35895)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEhaKf_yRcQLCYAHRsUp3gG9TnUHLKtvcU8wxVp-9UlbRpc6DoPSUH45QDcjJYhdve9Ufl_LX8By0DE_7M_IbiBWmWDyBi8eydF2qgryBRp6SAGYTSSNvwFn8jjbNu6910_BfcOe1e6pXlu-ZFyihDaO0dYHqJklE1PdRgBT6u0XsLoM4mcmcOg=w200-h200" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51170" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tetrasilsesquioxane cage (CHEBI:51170)"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWeVWC5J4elaJ2lpGGMMxZNPAeUVcucmqJbS46wNjSFpejBbDjI5EjuelxGhm6-QQFNYawbwlk0C4IJChJvy6rw1bqdx2MgMAM4u5AlCvr8s5_3a8CECVy75IVNMRFD2hktgdsUQ/w200-h200/tetrasilsesquioxane_cage.png" width="200" /></a></td>
</tr>
<tr><th align="center">(f)</th> <th align="center">(g)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="6" type="a">
<li> white phosphorus (<i>trivial</i>) <br />
<i>tetrahedro</i>-tetraphosphorus (<i>polynuclear cluster</i>) <br />
[<i>T</i><sub>d</sub>-(13)-Δ<sup>4</sup>-<i>closo</i>]tetraphosphorus (<i>polynuclear cluster, CEP descriptor</i>) <br />
tricyclo[1.1.0.0<sup>2,4</sup>]tetraphosphane (<i>von Baeyer</i>) <br />
tetraphosphy-[04.0<sup>1,3</sup>0<sup>2,4</sup>]tricycle (<i>ICR</i>)
</li>
<li> 2,4,6,8,9,10-hexaoxa-1,3,5,7-tetrasilatricyclo[3.3.1.1<sup>3,7</sup>]decane (<i>von Baeyer + replacement</i>) <br />
tricyclo[3.3.1.1<sup>3,7</sup>]tetrasiloxane (<i>von Baeyer for ring systems consisting of repeating units</i>) <br />
1,3,5,7-tetrahydrido-2,4,6,8,9,10-hexaoxy-1,3,5,7-tetrasily-[08.1<sup>1,5</sup>1<sup>3,7</sup>]tricycle (<i>ICR</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Similarly, nodal descriptors for polycyclic structures consist of two parts divided by the full stop. The first numeral corresponds to the number of nodes in the <i>main ring</i>, that is, the ring with the largest number of nodes. To indicate that the descriptor is for a cyclic structure, this numeral is preceded by a zero. Thus, ‘04’ for the structure <b>(f)</b> and ‘08’ for <b>(g)</b>. The numerals after the full stop specify the bridges. In <b>(f)</b>, the bridges contain no nodes and so are indicated by zeros with pairs of superscript locants, viz. ‘0<sup>1,3</sup>’ and ‘0<sup>2,4</sup>’, so the complete descriptor is ‘[04.0<sup>1,3</sup>0<sup>2,4</sup>]’<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup> and the ICR name is <span style="background-color: gold;">tetraphosphy</span>-[04.0<sup>1,3</sup>0<sup>2,4</sup>]tricycle. In <b>(g)</b>, the bridges contain one node each and therefore are indicated as ‘1<sup>1,5</sup>’ and ‘1<sup>3,7</sup>’ which gives us the complete descriptor ‘[08.1<sup>1,5</sup>1<sup>3,7</sup>]’<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup> and the name 1,3,5,7-<span style="background-color: lightgreen;">tetrahydrido</span>-2,4,6,8,9,10-<span style="background-color: gold;">hexaoxy</span>-1,3,5,7-<span style="background-color: gold;">tetrasily</span>-[08.1<sup>1,5</sup>1<sup>3,7</sup>]tricycle. </p>
<p> ICR nomenclature uses the combining forms ‘catenium’ and ‘cyclium’ for cations and ‘catenate’ and ‘cyclate’ for anions. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35898" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tetraphosphorus(1+) (CHEBI:35898)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEgCTJdWee_lmTBXq4Mum91jLYibK_4arvhuJb0FEmAv-oLODOTlWcZ-X-IG_9oHlV6mybVC3pDFyh6BRZ3bkuDrYmu6yYYNw5cVcE-HJfRKwCjzIFq0Upu_ZTPz_lHqHdsQPsBPVtegfG00qDKZ5JMtRYDXZUimcO_O011KfbPJUq_1uZt3YZ0=w200-h200" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18036" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="triphosphate(5−) (CHEBI:18036)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/a/AVvXsEjYMasjOKwAhzCaekB-1W-C-9jvAlwHJ_K6QSomHqYtNlCpsS0PLE0eLDzicHhggHbkYMtcxOLwcQ8j4kenm7e-Oekc_LfM40T379mUxKU1lMJt9fQ2VHG0FRxeY50uGoXVT-uRFDYPdvJ2BAsDbyE87p6fgK_wbm5pSibLYeWKpLufdhWQ5Vk=w200-h200" width="200" /></a></td>
</tr>
<tr><th align="center">(h)</th> <th align="center">(i)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="8" type="a">
<li> <i>tetrahedro</i>-tetraphosphorus(1+) (<i>polynuclear cluster</i>) <br />
[<i>T</i><sub>d</sub>-(13)-Δ<sup>4</sup>-<i>closo</i>]tetraphosphorus(1+) (<i>polynuclear cluster, CEP descriptor</i>) <br />
tricyclo[1.1.0.0<sup>2,4</sup>]tetraphosphanium (<i>von Baeyer</i>) <br />
tetraphosphy-[04.0<sup>1,3</sup>0<sup>2,4</sup>]tricyclium(1+) (<i>ICR</i>) </li>
<li> <i>catena</i>-triphosphate (<i>trivial</i>) <br />
bis(tetraoxidophosphato)dioxidophosphate(5−) (<i>additive</i>) <br />2,2,4,4,6,6-hexaoxido-1,3,5,7-tetraoxy-2,4,6-triphosphy-[7]catenate(5−) (<i>ICR</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> So <b>(h)</b>, the monocationic form of white phosphorus <b>(f)</b>, is named <span style="background-color: gold;">tetraphosphy</span>-[04.0<sup>1,3</sup>0<sup>2,4</sup>]tricyclium(1+). The structure <b>(i)</b>, the fully deprotonated form of <i>catena</i>-triphosphoric acid <b>(c)</b>, is named 2,2,4,4,6,6-<span style="background-color: lightgreen;">hexaoxido</span>-1,3,5,7-<span style="background-color: gold;">tetraoxy</span>-2,4,6-<span style="background-color: gold;">triphosphy</span>-[7]catenate(5−). </p>
<p> The recommendations [<a href="#Fluck_and_Laitinen_1997" title="Fluck & Laitinen (1997)">1</a>] are a quarter century old already and I think it’s fair to say that this nomenclature didn’t exactly catch on. Why? For one thing, the names generated according to it are just too long to be “practical”. Given that the optimal <a href="http://en.wikipedia.org/wiki/Line_length" target="_blank" title="Line length in Wikipedia">line length</a> in most printed texts is between 60 and 70 characters per line, the ICR names for even simple molecules won’t fit a single line; e.g., the name 1,7-dihydrido-2,4,6-trihydroxido-2,4,6-trioxido-1,3,5,7-tetraoxy-2,4,6-triphosphy-[7]catena <b>(c)</b> contains 91 characters. For another thing, the superficial similarity of nodal descriptors to well-established von Baeyer descriptors <strike>can be</strike> is quite confusing. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> Note those terminal ‘<span style="background-color: lightgreen;">hydrido</span>’ ligands attached to the terminal oxygen atoms: in this way, the name is based on the longest chain in the molecule. Otherwise, <b>(c)</b> could be called 1,1,3,5,5-<span style="background-color: lightgreen;">pentahydroxido</span>-1,3,5-<span style="background-color: lightgreen;">trioxido</span>-2,4-<span style="background-color: gold;">dioxy</span>-1,3,5-<span style="background-color: gold;">triphosphy</span>-[5]catena. This name is shorter than 1,7-<span style="background-color: lightgreen;">dihydrido</span>-2,4,6-<span style="background-color: lightgreen;">trihydroxido</span>-2,4,6-<span style="background-color: lightgreen;">trioxido</span>-1,3,5,7-<span style="background-color: gold;">tetraoxy</span>-2,4,6-<span style="background-color: gold;">triphosphy</span>-[7]catena but, you may have noticed already, ICR nomenclature is not about giving shortest names. </td></tr>
<tr><td valign="top">†</td>
<td> In ICR nomenclature, organic substituents such as ‘methyl’ are treated as ligands and do not form part of chain. </td></tr>
<tr><td valign="top">‡</td>
<td> Note that here, in contrast to von Baeyer descriptors, the numerals indicating the bridges are <i>not</i> separated by full stops. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Fluck_and_Laitinen_1997"></a>
<li> Fluck, E.O. and Laitinen, R.S. (1997) Nomenclature of inorganic chains and ring compounds (IUPAC Recommendations 1997). <a href="http://doi.org/10.1351/pac199769081659" target="_blank" title="Fluck and Laitinen (1997) Pure Appl. Chem. 69, 1659-1692."><i>Pure and Applied Chemistry</i> <b>69</b>, 1659—1692</a>. </li>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
<a name="Powell_1984"></a>
<li> Powell, W.H. (1984) Treatment of variable valence in organic nomenclature (lambda convention) (Recommendations 1983).
<a href="http://doi.org/10.1351/pac198456060769" target="_blank" title="Powell (1984) Pure Appl. Chem. 56, 769-778."><i>Pure and Applied Chemistry</i> <b>56</b>, 769—778</a>. </li></ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-43594599381574540432021-11-14T22:00:00.046+00:002023-08-06T21:02:06.743+01:00Phane names<p> Have a look at the structure <b>(a)</b>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51202" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="calix[4]arene (CHEBI:51202)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2Qioi8f36w7pPSNJMFp0VjayqSrML4vWp2wLV-owysG20jwKTBK7YJx1wjJNqQEVKJVMQ6cDulw1Mb3Py8qncS0b_t5AGRxO_vV8mLrTH8JPbUM7Wy8HYLI5jo0TXdue8hTfpOw/w200-h200/calix-4-arene.png" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> calix[4]arene (<i>trivial</i>) <br />
pentacyclo[19.3.1.1<sup>3,7</sup>.1<sup>9,13</sup>.1<sup>15,19</sup>]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene (<i>von Baeyer</i>) <br />
1,3,5,7(1,3)-tetrabenzenacyclooctaphane (<i>phane</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Applying <a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog">von Baeyer nomenclature</a>, we get a horrendously long and unwieldy name ‘pentacyclo[19.3.1.1<sup>3,7</sup>.1<sup>9,13</sup>.1<sup>15,19</sup>]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene’. I think it’s a crime to name a beautifully symmetrical structure like <b>(a)</b> in such a fashion. Can’t we create a name that states the obvious: <b>(a)</b> is a big cycle containing four benzene rings? </p>
<a name='more'></a>
<p> I think we not just can but also should. And IUPAC provides an instrument for that in the form of <i>phane nomenclature</i> [<a href="#Powell_1998" title="Powell (1998)">1</a>, <a href="#Favre_et_al_2002" title="Favre et al. (2002)">2</a>]. Let’s start with cyclooctane <b>(b)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://chem.nlm.nih.gov/chemidplus/number/292-64-8" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclooctane (CAS 292-64-8)"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjywylx53bjkXQan-oCOkf6pI-InKouyoN1O5tSg0exCLyKwwMAGzdghjIYXGTvY9OVrHq9u3dMIG1SgTyPtXOmjAgtRVOfurMDFBSy6DhrsH0wMecJHXrpTBMQQZHXuWD24-Ct0A/w200-h200/cyclooctane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="2" type="a">
<li> cyclooctane </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Now let us replace the atoms at positions 1, 3, 5 and 7 of cyclooctane by fat black dots thus <b>(c)</b>: </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZSn5R3Q8-wHiIAz-sXsnKmVM9cBWB9dv4tU9v_Mi34c8R5C2b0kLvBB8s8jmfDfOyMlkorNL3uV80LTMimKmDoBdALei8Tf6FvNDHszqQvtmazseBXQxM5U6Wpg5CWtjvkaT48w/s600/cyclooctaphane.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiZSn5R3Q8-wHiIAz-sXsnKmVM9cBWB9dv4tU9v_Mi34c8R5C2b0kLvBB8s8jmfDfOyMlkorNL3uV80LTMimKmDoBdALei8Tf6FvNDHszqQvtmazseBXQxM5U6Wpg5CWtjvkaT48w/w200-h200/cyclooctaphane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> cyclooctaphane </li>
</ol>
</td>
</tr>
</table>
</center>
<p> These fat black dots represent so-called <i>superatoms</i><sup><a href="#Footnote_*" title="Footnote *">*</a></sup> that can be replaced by ring structures in an operation known as <i>amplification</i> [<a href="#Powell_1998" title="Powell (1998)">1</a>, <a href="#Favre_et_al_2002" title="Favre et al. (2002)">2</a>]. These ring structures are called <i>amplificants</i>. The name constructed in such a way is based on a “simplified skeletal name” which is basically a name of a parent hydride, e.g. <span style="background-color: yellow;">cyclooctane</span> <b>(b)</b>, modified to contain ‘phane’, e.g. <span style="background-color: yellow;">cycloocta</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. Adding the locants for superatoms yields 1,3,5,7-tetra<span style="background-color: yellow;">cycloocta</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span> <b>(c)</b>. If we replace superatoms by <span style="background-color: palegreen;">benzene</span> rings, we get 1,3,5,7-<span style="background-color: palegreen;">tetrabenzena</span><span style="background-color: yellow;">cycloocta</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. The recommendations [<a href="#Powell_1998" title="Powell (1998)">1</a>, <a href="#Favre_et_al_2002" title="Favre et al. (2002)">2</a>] refer to word parts such as ‘<span style="background-color: palegreen;">benzena</span>’ as “amplification prefixes”, although the reader may already have guessed that they are in fact <a href="http://metallome.blogspot.com/2020/10/prefixes-or-combining-forms.html" target="_blank" title="Prefixes — or combining forms? @ this blog">combining forms</a><sup><a href="#Footnote_†" title="Footnote †">†</a></sup>. If we want to specify that all benzene rings are attached at positions 1 and 3, we add these locants in parentheses following the superatom locants: 1,3,5,7(1,3)-<span style="background-color: palegreen;">tetrabenzena</span><span style="background-color: yellow;">cycloocta</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. </p>
<p> While replacing superatoms of <b>(c)</b> by <span style="background-color: palegreen;">furan</span>s attached at positions 2 and 5, we get 1,3,5,7(2,5)-<span style="background-color: palegreen;">tetrafurana</span><span style="background-color: yellow;">cycloocta</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span> <b>(d)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51407" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="calix[4]furan (CHEBI:51407)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivhc-VZRuDP9Grdyf80VDmugqaK5tDfT2klCS38TxmzkWBz6zacCfmQwKMQ8sc06MT8gMnSmNIOccuh-_ECHL5veOk1tG3dn9ToDX0M2IdqE69olYTot_X1lZcbsz8JxFiRO85eA/w200-h200/calix-4-furan.png" width="200" /></a></td>
</tr>
<tr><th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="4" type="a">
<li> calix[4]furan (<i>trivial</i>) <br />
21,22,23,24-tetraoxapentacyclo[16.2.1.1<sup>3,6</sup>.1<sup>8,11</sup>.1<sup>13,16</sup>]tetracosa-1(20),3,5,8,10,13,15,18-octaene (<i>von Baeyer</i>) <br />
1,3,5,7(2,5)-tetrafuranacyclooctaphane (<i>phane</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Phane nomenclature can be easily combined with <a href="http://metallome.blogspot.com/2020/06/skeletal-replacement-nomenclature.html" target="_blank" title="Skeletal replacement nomenclature @ this blog">skeletal replacement nomenclature</a>. For instance, oxacalix[4]arene <b>(e)</b> is calix[4]arene <b>(a)</b> with four carbons replaced by oxygens. So we get the phane name for <b>(e)</b> by simply sticking ‘2,4,6,8-<span style="background-color: paleturquoise;">tetraoxa</span>’ in front of the phane name for <b>(a)</b>, thus 2,4,6,8-<span style="background-color: paleturquoise;">tetraoxa</span>-1,3,5,7(1,3)-<span style="background-color: palegreen;">tetrabenzena</span><span style="background-color: yellow;">cycloocta</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51204" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="oxacalix[4]arene (CHEBI:51204)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEUQ-pz607hKIVNuhnN7pEEOT32Q7EnmmC7ASZPFEfpzP83WjQvr60I9-0Cs-Thrw3n0JCt90DSFeQDstTVwJzVgLpwkCdzBFxnLLd4vYEr1En8u9r6K5ViiKhCQwGwGavRtzVUw/w200-h200/oxacalix-4-arene.png" width="200" /></a></td>
</tr>
<tr><th align="center">(e)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> oxacalix[4]arene (<i>trivial</i>) <br />
2,8,14,20-tetraoxapentacyclo[19.3.1.1<sup>3,7</sup>.1<sup>9,13</sup>.1<sup>15,19</sup>]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene (<i>von Baeyer + replacement</i>) <br />
2,4,6,8-tetraoxa-1,3,5,7(1,3)-tetrabenzenacyclooctaphane (<i>phane + replacement</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Likewise, we can derive the phane name for <b>(f)</b> starting from <span style="background-color: yellow;">hexane</span> <b>(g)</b>. Here, all six carbon atoms of hexane are replaced by superatoms, thus hexa<span style="background-color: yellow;">hexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>; replacing superatoms with <span style="background-color: palegreen;">pyridine</span> rings results in <span style="background-color: palegreen;">hexapyridina</span><span style="background-color: yellow;">hexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>; indicating the points of attachments for pyridine rings, we get 1,6(2),2,3,4,5(2,5)-<span style="background-color: palegreen;">hexapyridina</span><span style="background-color: yellow;">hexa</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>. The advantage of this name over the ring assembly names is the absence of primes or superscripts. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:59703" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2,2':6',2'':6'',2''':6''',2'''':6'''',2'''''-sexipyridine (CHEBI:59703)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgu3XZzi-Je7m-9KIGtrWszu9BFGm2lXD5GHgDmhij79T68EkwPUNoEqUf9jo4xdTzQBqBKiu1YF7t2mahx0vYjS8pp_AJf2gxs-ewnshUthE-Qvclt3-2i5Ph1kn9A76E_kGqsmw/w200-h200/sexipyridine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29021" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="hexane (CHEBI:29021)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsF_s5CogGCtVEjdxkS7cuOvQhMfPOPXiGy8ZBuXPIwxvQSAOzWF-s0vC64ewujlChH2ALtSzOvINmBUzC4ip9oBEJJ_ih7trUc2-Tecsa42zgfeRwGEolt32pNkQ1v3DBl0gX8Q/s0/hexane.png" /></a></td>
</tr>
<tr><th align="center">(f)</th> <th align="center">(g)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="6" type="a">
<li> 2,2′:6′,2′′:6′′,2′′′:6′′′,2′′′′:6′′′′,2′′′′′-sexipyridine (<i>ring assembly</i>) <br />
1<sup>2</sup>,2<sup>2</sup>:2<sup>6</sup>,3<sup>2</sup>:3<sup>6</sup>,4<sup>2</sup>:4<sup>6</sup>,5<sup>2</sup>:5<sup>6</sup>,6<sup>2</sup>-sexipyridine (<i>ring assembly, PIN</i>) <br />
1,6(2),2,3,4,5(2,5)-hexapyridinahexaphane (<i>phane</i>) </li>
<li> hexane </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Nothing prevents us from creating phane names using <i>non-identical</i> amplificants. Consider UCL 1684 <b>(h)</b>, a potent blocker of small conductance Ca<sup>2+</sup>-activated K<sup>+</sup> (SK<sub>Ca</sub>) channels [<a href="#Rosa_et_al_1998" title="Rosa et al (1998)">3</a>]: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51204" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="UCL 1684 (CHEBI:35040)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWY4IXVk0MHN1rsCWwY7FqeQBJe_US_Nxv718qKBN-Iu-ck_Tf2m5gtSGQvldaBp6sTvBHu_RL-LzwbObh4Fcd5Pyj5CUky-yYkUPl344chrJahWGRye90-lw7Gw45NYM-vlf04Q/w200-h200/UCL1684.png" width="200" /></a></td>
</tr>
<tr><th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="8" type="a">
<li> UCL 1684 (<i>trivial</i>) <br />
17,24-diaza-1,9-diazoniaheptacyclo[23.6.2.2<sup>9,16</sup>.2<sup>19,22</sup>.1<sup>3,7</sup>.0<sup>10,15</sup>.0<sup>26,31</sup>]octatriaconta-1(32),3(38),4,6,9(37),10(15),11,13,16(36),19,21,25(33),26(31),27,29,34-hexadecaene (<i>von Baeyer + replacement</i>) <br />
1<sup>1</sup>λ<sup>5</sup>,5<sup>1</sup>λ<sup>5</sup>-6,10-diaza-3(1,3),8(1,4)-dibenzena-1,5(1,4)-diquinolinacyclodecaphane-1<sup>1</sup>,5<sup>1</sup>-bis(ylium) (<i>phane + replacement</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> The structure <b>(h)</b> can be thought of as a <span style="background-color: yellow;">cyclodecane</span> where atoms 1 and 5 are replaced by <span style="background-color: palegreen;">quinoline</span> rings, atoms 3 and 8 replaced by <span style="background-color: palegreen;">benzene</span> rings, and atoms 6 and 10 replaced by <span style="background-color: paleturquoise;">nitrogen</span> atoms. The resulting phane name is 1<sup>1</sup>λ<sup>5</sup>,5<sup>1</sup>λ<sup>5</sup>-6,10-<span style="background-color: paleturquoise;">diaza</span>-3(1,3),8(1,4)-<span style="background-color: palegreen;">dibenzena</span>-1,5(1,4)-<span style="background-color: palegreen;">diquinolina</span><span style="background-color: yellow;">cyclodeca</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>-1<sup>1</sup>,5<sup>1</sup>-<span style="background-color: lavender;">bis(ylium)</span><sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>. It sure is long but still easier to read and interpret than von Baeyer name 17,24-diaza-1,9-diazoniaheptacyclo[23.6.2.2<sup>9,16</sup>.2<sup>19,22</sup>.1<sup>3,7</sup>.0<sup>10,15</sup>.0<sup>26,31</sup>]octatriaconta-1(32),3(38),4,6,9(37),10(15),11,13,16(36),19,21,25(33),26(31),27,29,34-hexadecaene. </p>
<p> Some observations. There is no special class of compounds named “phanes”. The only thing all the structures that we can name as ‘phanes’ have in common is that they contain rings. For structures with many identical rings, phane nomenclature can give us shorter names compared to those offered by other methods. </p>
<p> The IUPAC recommendations say that “a phane replacement operation <...> represents an extension of the traditional skeletal replacement technique” [<a href="#Powell_1998" title="Powell (1998)">1</a>]. Why can’t we name then the structure <b>(a)</b> simply 1,3,5,7(1,3)-<span style="background-color: palegreen;">tetrabenzena</span><span style="background-color: yellow;">cyclooctane</span>, rather than 1,3,5,7(1,3)-<span style="background-color: palegreen;">tetrabenzena</span><span style="background-color: yellow;">cycloocta</span><span style="background-color: gainsboro;">pha</span><span style="background-color: yellow;">ne</span>? Knowing that the combining form ‘<span style="background-color: palegreen;">benzena</span>’ is used for a replacement operation should be enough. As paradoxical it may sound, in phane nomenclature the ‘phane’ bit itself is redundant. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> The meaning of “superatom” in phane nomenclature is completely different from that of <a href="http://en.wikipedia.org/wiki/Superatom" target="_blank" title="Superatom in Wikipedia">superatom</a> in inorganic chemistry. </td></tr>
<tr><td valign="top">†</td>
<td> “Amplification prefixes” are not prefixes because they contain content morphemes. For example, ‘<span style="background-color: palegreen;">benzena</span>’ could be analysed as the base ‘benzen’ plus the functional morpheme ‘a’; in its turn, ‘benzen’ consists of the roots ‘benz’ and ‘en’. </td></tr>
<tr><td valign="top">‡</td>
<td> The descriptors 1<sup>1</sup>λ<sup>5</sup>,5<sup>1</sup>λ<sup>5</sup> indicate that the nitrogen atoms at the position 1 of quinoline rings have the <a href="http://metallome.blogspot.com/2023/04/lambda-convention.html" target="_blank" title="λ-convention @ this blog">non-standard bonding number</a> of five [<a href="#Powell_1984" title="Powell (1984)">4</a>]. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Powell_1998"></a>
<li> Powell, W.H. (1998) Phane nomenclature. Part I: Phane parent names (IUPAC Recommendations 1998). <a href="http://doi.org/10.1351/pac199870081513" target="_blank" title="Powell (1998) Pure Appl. Chem. 70, 1513-1545."><i>Pure and Applied Chemistry</i> <b>70</b>, 1513—1545</a>. </li>
<a name="Favre_et_al_2002"></a>
<li> Favre, H.A., Hellwinkel, D., Powell, W.H., Smith, H.A. and Tsay, S.S.-C. (2002) Phane nomenclature. Part II. Modification of the degree of hydrogenation and substitution derivatives of phane parent hydrides (IUPAC Recommendations 2002). <a href="http://doi.org/10.1351/pac200274050809" target="_blank" title="Favre et al. (2002) Pure Appl. Chem. 74, 809-834."><i>Pure and Applied Chemistry</i> <b>74</b>, 809—834</a>. </li>
<a name="Rosa_et_al_1998"></a>
<li> Rosa, J.C., Galanakis, D., Ganellin, C.R., Dunn, P.M. and Jenkinson, D.H. (1998) Bis-quinolinium cyclophanes: 6,10-diaza-3(1,3),8(1,4)-dibenzena-1,5(1,4)-diquinolinacyclodecaphane (UCL 1684), the first nanomolar, non-peptidic blocker of the apamin-sensitive Ca<sup>2+</sup>-activated K<sup>+</sup> channel. <a href="http://doi.org/10.1021/jm970571a" target="_blank" title="Rosa et al. (1998) J. Med. Chem. 41, 2-5."><i>Journal of Medicinal Chemistry</i> <b>41</b>, 2—5</a>. </li>
<a name="Powell_1984"></a>
<li> Powell, W.H. (1984) Treatment of variable valence in organic nomenclature (lambda convention) (Recommendations 1983).
<a href="http://doi.org/10.1351/pac198456060769" target="_blank" title="Powell (1984) Pure Appl. Chem. 56, 769-778."><i>Pure and Applied Chemistry</i> <b>56</b>, 769—778</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-56485776757043893222021-07-29T10:00:00.022+01:002023-08-07T09:55:00.628+01:00Ring assemblies<p> How shall we call the structure <b>(a)</b>?</p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17097" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="biphenyl (CHEBI:17097)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEieRxwNSShenEsMIbchvKf-jR41APFO6sWt48EwbbqZ4no7GaANWDHYXji1i6X_dLNVHpTeUS1uUZVbwNpXO9JynpywQ04GZjH9llOxZ60nTYQZvaestvantM-eBu2xqTyBvR3zlw/w200-h200/biphenyl.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> biphenyl (<i>trivial</i>) <br />
1,1′-biphenyl (<i>ring assembly, <a href="http://en.wikipedia.org/wiki/Preferred_IUPAC_name" target="_blank" title="Preferred IUPAC name in Wikipedia">PIN</a></i>) <br />
phenylbenzene (<i>substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> We can name it <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">substitutively</a>, i.e. substituting one hydrogen atom in the parent hydride <span style="background-color: yellow;">benzene</span> with <span style="background-color: lavender;">phenyl</span> group: <span style="background-color: lavender;">phenyl</span><span style="background-color: yellow;">benzene</span>. This name, however, does not reflect the obvious symmetry of the molecule. </p>
<p> Similar story with <b>(b)</b> whose substitutive name, <span style="background-color: lavender;">cyclopentylidene</span><span style="background-color: yellow;">cyclopentane</span>, is barely pronounceable. </p>
<a name='more'></a>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36822" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,1'-bi(cyclopentylidene) (CHEBI:36822)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQwZ3icEDSBjldNyBoctJkpKLo5-FkzGkQZi6JXVo9M1Ce3q4Xk4ufnz-8a7ggWAxj4zKf6ZZAZFjQjgf-zHKntTb-K8lfAarJInDgM3RqOMv4A7vDJMjmeYDpzMCdFBfkyyxCQw/w200-h200/1%252C1%2527-bicyclopentylidene.png" width="200" /></a></td></tr>
<tr><th align="center">(b)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="2" type="a">
<li> 1,1′-bi(cyclopentylidene) (<i>ring assembly</i>) <br />
cyclopentylidenecyclopentane (<i>substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The structures <b>(a)</b> and <b>(b)</b> are examples of <a href="http://goldbook.iupac.org/terms/view/R05393" target="_blank" title="ring assembly in Gold Book"><i><i>ring assemblies</i></i></a>, that is, systems where two ring components with no atoms in common are directly connected by a single [as in <b>(a)</b>] or a double [as in <b>(b)</b>] covalent bond<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. </p>
<p> Ring assemblies consisting of <i>identical</i> ring components can be named by combining the name of the component with a multiplier. For example, <b>(a)</b> contains two <span style="background-color: lavender;">phenyl</span> groups and known as 1,1′-bi<span style="background-color: lavender;">phenyl</span>; <b>(b)</b> contains two <span style="background-color: lavender;">cyclopentylidene</span> groups and named 1,1′-bi(<span style="background-color: lavender;">cyclopentylidene</span>). Now ‘1,1′’ bit appears to be redundant since there is only one way of connecting two phenyl (or two cyclopentylidene) groups by a direct bond. However, we do need locants in most of ring assemblies to avoid ambiguity. Compare the structures <b>(c)</b> and <b>(d)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30351" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2,2'-bipyridine (CHEBI:30351)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLgjqnoqg6ElLfgzCgOgswUBbu3dCsp5z6ufk48tM74E3Sw1rikKCBsJxoUv0GUhbiTFvCD5pr1CToV-SGktV6mrJuNFMD6CxpBQe_mG0owzb2QJpH4WrkVK14fZDFW4EOFliunA/w200-h200/2%252C2%2527-bipyridine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30985" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="4,4'-bipyridine (CHEBI:30985)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiI-OBlhyGn3NGlBhkMNZVRo0FyqOrE7dJcBySeTOb5S5lYZNjxO7mfenbTTFVnqMgJI-5lsN9czTF0wwhL2KXe_WrLLunQ90goPo82h3p4e7K2SCnXVijB6mBGaYvCmQOPYo8-5A/w200-h200/4%252C4%2527-bipyridine.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> 2,2′-bipyridine (<i>ring assembly, PIN</i>) <br />
2,2′-bipyridyl (<i>ring assembly</i>) </li>
<li> 4,4′-bipyridine (<i>ring assembly, PIN</i>) <br />
4,4′-bipyridyl (<i>ring assembly</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Do these names remind you <a href="http://metallome.blogspot.com/2020/09/multiplicative-names.html" target="_blank" title="Multiplicative names @ this blog">multiplicative names</a>? This is because they are built almost exactly like multiplicative names, except there are no linkers. Oh, and instead of Greek-derived multipliers ‘di’, ‘tri’, ‘tetra’, etc., the Latin-derived multipliers are used: </p>
<center>
<table>
<tr><th>2</th> <td> bi </td></tr>
<tr><th>3</th> <td> ter </td></tr>
<tr><th>4</th> <td> quater </td></tr>
<tr><th>5</th> <td> quinque </td></tr>
<tr><th>6</th> <td> sexi </td></tr>
<tr><th>7</th> <td> septi </td></tr>
<tr><th>8</th> <td> octi </td></tr>
<tr><th>9</th> <td> novi </td></tr>
<tr><th>10</th> <td> deci </td> </tr>
<tr><th>11</th> <td> undeci </td> </tr>
<tr><th>12</th> <td> dodeci </td> </tr>
</table>
</center>
<p> You may have noticed that ring assemblies named in this fashion can contain either unchanged parent hydride name, as in 2,2′-bi<span style="background-color: yellow;">pyridine</span>, or a substituent group name, as in 2,2′-bi<span style="background-color: lavender;">pyridyl</span>. The former method is preferred (i.e. used to create PINs) in most ring assembies; the later is used for assembiles of benzene rings, as in <b>(a)</b>, and for rings linked by a double bond, as in <b>(b)</b> [<a href="#Blue_Book_2014" name="Blue Book (2014)">1</a>]. On the other hand, CAS always names the ring assemblies linked by a double bond substitutively [<a href="#Bünzli-Trepp_2007" name="Bünzli-Trepp (2007)">2</a>]. </p>
<p> As soon as there are three or more ring components in an assembly, the names start to lose elegance. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:50089" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2,3':4',2''-terthiophene (CHEBI:50089)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmiCtlL8PKbCp5S2DuVdE1Y0DSJzicHILPzyZa9p7jg7_Q-Pv3gjRlKgAhDnKvxgzd7cZDT7MA75t-ukiLVdVx_xhRJA04lj76ArOGTZqNOYi7qBbF38mPeWfMJcdhmb3MwO4yQA/w200-h200/2%252C3%2527-4%2527%252C2%2527%2527-terthiophene.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:52240" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="p-quaterphenyl (CHEBI:52240)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiPuwuHXeEH6kdZnaDenfohgU9nnRNvFXAFWvPd-QmL23EfsHIDrUDnvFDu4j2cSF4hxoDM6rp9-IVCxR717IsX8n8auXhrj5K6kYsFHEz9kl_cDuujWf-rpBcGtKveBCFRX0TofA/w200-h200/quadriphenyl.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:59703" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2,2':6',2'':6'',2''':6''',2'''':6'''',2'''''-sexipyridine (CHEBI:59703)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgu3XZzi-Je7m-9KIGtrWszu9BFGm2lXD5GHgDmhij79T68EkwPUNoEqUf9jo4xdTzQBqBKiu1YF7t2mahx0vYjS8pp_AJf2gxs-ewnshUthE-Qvclt3-2i5Ph1kn9A76E_kGqsmw/w200-h200/sexipyridine.png" width="200" /></a></td>
</tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th> <th align="center">(g)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> 2,3′:4′,2′′-terthiophene (<i>ring assembly</i>) <br />
1<sup>2</sup>,2<sup>3</sup>:2<sup>4</sup>,3<sup>2</sup>-terthiophene (<i>ring assembly, PIN</i>) </li>
<li> benzerythrene (<i>trivial</i>) <br />
1,1′:4′,1′′:4′′,1′′′-quaterphenyl (<i>ring assembly</i>) <br />
1<sup>1</sup>,2<sup>1</sup>:2<sup>4</sup>,3<sup>1</sup>:3<sup>4</sup>,4<sup>1</sup>-quaterphenyl (<i>ring assembly, PIN</i>) <br />
4,4′-diphenyl-1,1′-biphenyl (<i>ring assembly + substitutive</i>) <br />
4,4′-bi-1,1′-biphenyl (<i>ring assembly + substitutive</i>) </li>
<li> 2,2′:6′,2′′:6′′,2′′′:6′′′,2′′′′:6′′′′,2′′′′′-sexipyridine (<i>ring assembly</i>) <br /> 1<sup>2</sup>,2<sup>2</sup>:2<sup>6</sup>,3<sup>2</sup>:3<sup>6</sup>,4<sup>2</sup>:4<sup>6</sup>,5<sup>2</sup>:5<sup>6</sup>,6<sup>2</sup>-sexipyridine (<i>ring assembly, PIN</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The locants in 2,3′:4′,2′′-terthiophene <b>(e)</b> simply indicate that the atom 2 in the first thiophene ring is linked to the atom 3 in the second thiophene ring, and the atom 4 in the second thiophene ring is linked to the atom 2 in the third thiophene ring. The name of <b>(f)</b>, 1,1′:4′,1′′:4′′,1′′′-quaterphenyl, follows the same logic. One may wonder if you can give it a shorter systematic name. For example, if we substitute each phenyl ring of one 1,1′-biphenyl by a phenyl group at position 4, we get 4,4′-diphenyl-1,1′-biphenyl. Alternatively, we can join two 1,1′-biphenyl molecules through the position 4 to get 4,4′-bi-1,1′-biphenyl. This is the shortest systematic name for <b>(f)</b> I can think of, yet I never seen it in any publication (until I put it in this post, that is). The problem is, IUPAC does not allow the ring assembly names, such as ‘1,1′-biphenyl’, as parent hydrides. </p>
<p> The systematic name of <b>(g)</b>, 2,2′:6′,2′′:6′′,2′′′:6′′′,2′′′′:6′′′′,2′′′′′-sexipyridine, is taking the primed locant system to the extreme. I mean, the Romans knew better than to use five ‘I’s for ‘five’. So in the New Blue Book IUPAC came up with a <i>different</i> system which is used to generate PINs for ring assemblies [<a href="#Blue_Book_2014" name="Blue Book (2014)">1</a>]. The rings are numbered sequentially (1, 2, 3, etc.) and the attachment points are indicated by superscript locants. Thus <b>(e)</b> is named 1<sup>2</sup>,2<sup>3</sup>:2<sup>4</sup>,3<sup>2</sup>-terthiophene, <b>(f)</b> 1<sup>1</sup>,2<sup>1</sup>:2<sup>4</sup>,3<sup>1</sup>:3<sup>4</sup>,4<sup>1</sup>-quaterphenyl, and <b>(g)</b> 1<sup>2</sup>,2<sup>2</sup>:2<sup>6</sup>,3<sup>2</sup>:3<sup>6</sup>,4<sup>2</sup>:4<sup>6</sup>,5<sup>2</sup>:5<sup>6</sup>,6<sup>2</sup>-sexipyridine. </p>
<p> The same basic approach can be used to name ring assemblies of identical <i>polycyclic</i> components: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:174128" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="5,5',6,6'-tetrahydroxy-3,3'-biindolyl (CHEBI:174128)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjE3tCZx74B-Nq5xkqBxntfRoDThE9HeDXvmydbowefvGvkouNulDsOY-Q2wvehuYYTcL-QgduYZJRUyWX6gN24o7l1CwejewL1WB6WOeys5q1msVwbOvZKH-f3oXjEReLF7cL0HQ/w200-h200/tetrahydroxybiindolyl.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:52563" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="5,5':15',5''-terporphyrin (CHEBI:52563)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAoUjIuiO6lUMD_fCNdLs2qKPmh-S6tfPy_WLco_zZBW7mqNHpG2wGSQfCkl7ZIXQwekt3_LvnxGOTnjAoRO5B1OobNmJUXrDWM4F8NS4eOo-Tzgo1TQNH3t4-FHqZOjWLKz57mA/w200-h200/terporphyrin.png" width="200" /></a></td></tr>
<tr><th align="center">(h)</th> <th align="center">(i)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="8" type="a">
<li> 1<i>H</i>,1′<i>H</i>-3,3′-biindole-5,5′,6,6′-tetrol (<i>ring assembly + substitutive</i>) </li>
<li> 5,5′:15′,5′′-terporphyrin (<i>ring assembly</i>) <br />
1<sup>5</sup>,2<sup>5</sup>:2<sup>15</sup>,3<sup>5</sup>-terporphyrin (<i>ring assembly, PIN</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Assemblies of <i>non-identical</i> ring components are named using simple substitutive nomenclature. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:167083" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="3-phenylfuran (CHEBI:167083)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzuWZILfEdwvILgVPh7whcuU77h8k6TPUQkvr2pxYa6SQLpeacMfszOccXWeph0H498fpLqLaO6VjGpjxE2-BFS8f3yQ8VEYGmwgWGhV_V1KPsVUdJAD6C3HFrVR-ZrpvbRquehQ/w200-h200/3-phenylfuran.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:50459" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2,5-diphenylfuran (CHEBI:50459)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhaHYhUNJBWTyfbObpcduB898tUfiU-RAMMJh-2zgUdrSeOq0n9GW5XHYZzi_e-UIFskwBP2ZvHLTS1GRyofW9owDbuABfUJu340XK6rzRWNyVfGBplaKt4q0mwSUxP_g4YQIwJ0g/w200-h200/2-5-diphenylfuran.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33111" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="apholate (CHEBI:33111)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWYzYhYWXCZmiYCc_yQxvRyxDlchRt2kLICACl2A662O-4tv5MM4kJagfv1-N6lFQzzH_9OZ3UYqF1_-v5aD6Qzp26RQkB1TvCjdcO1PUs1L-ppPg1ShLtLWvM5FSXYVXn5dRWNA/w200-h200/apholate.png" width="200" /></a></td></tr>
<tr><th align="center">(j)</th> <th align="center">(k)</th> <th align="center">(l)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="10" type="a">
<li> 3-phenylfuran (<i>substitutive</i>) </li>
<li> 2,5-diphenylfuran (<i>substitutive</i>) </li>
<li> apholate (<i>trivial</i>) <br />
2,2,4,4,6,6-hexakis(aziridin-1-yl)-1,3,5,2λ<sup>5</sup>,4λ<sup>5</sup>,6λ<sup>5</sup>-triazatriphosphinine (<i>H-W + substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<a name="Footnote_*"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> I see no reason why the IUPAC definition can’t be extended to include a <i>triple</i> bond linking cyclic components. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Blue_Book_2014">
</a><li><a name="Blue_Book_2014"> Favre, H.A. and Powell, W.H. </a><a href="https://amzn.to/3ej1Mag" target="_blank" title="Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names @ Amazon.co.uk"><i>Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names</i></a>. Royal Society of Chemistry, Cambridge, 2014. </li>
<a name="Bünzli-Trepp_2007">
</a><li><a name="Bünzli-Trepp_2007"> Bünzli-Trepp, U. </a><a href="https://amzn.to/322u1X4" target="_blank" title="Systematic Nomenclature of Organic, Organometallic and Coordination Chemistry @ Amazon.co.uk"><i>Systematic Nomenclature of Organic, Organometallic and Coordination Chemistry</i></a>. EPFL Press, 2007, pp. 141—144. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-77590326656271455082021-06-28T13:00:00.062+01:002023-08-07T09:56:43.147+01:00Spiro names<p> Observe the structure <b>(a)</b>. Doesn’t it look like our old friend <a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog">housane</a> after a tornado? It kept its roof but only just. </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDBXIyWrZJ31J5S5zUvgQS3zuvzfLchpTJHZMTZ4CzGAUcYp9f8DDBZbDqOEBOgI27HMnb1kCoUwCFLtj5TQKCDnYve8nqJ85mgTWQqK6dLvKfkOURY2o6rKVkkwfN2rNZ6XiH-Q/s600/spirohexane.png" style="margin-left: 1em; margin-right: 1em;" target="_blabk" title="spiro[2.3]hexane"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDBXIyWrZJ31J5S5zUvgQS3zuvzfLchpTJHZMTZ4CzGAUcYp9f8DDBZbDqOEBOgI27HMnb1kCoUwCFLtj5TQKCDnYve8nqJ85mgTWQqK6dLvKfkOURY2o6rKVkkwfN2rNZ6XiH-Q/w200-h200/spirohexane.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="1" type="a">
<li> spiro[2.3]hexane <br />
spirohexane </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Let us number it in the following fashion: </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiM1VR20Iyw3Hmwb01aCzU68JrOIaM1ZPJ49bhcNWAfbpsIlMyoNMByDC5ZV2e6nmlxjOAv_URbfhjdfn7ijHcrNBm9kKboLFv4teOhwdBnevAFl_aJ-x3fY62PB3A9VjCrGDZVaA/s600/spirohexane.png" style="margin-left: 1em; margin-right: 1em;" target="_blabk" title="spiro[2.3]hexane"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiM1VR20Iyw3Hmwb01aCzU68JrOIaM1ZPJ49bhcNWAfbpsIlMyoNMByDC5ZV2e6nmlxjOAv_URbfhjdfn7ijHcrNBm9kKboLFv4teOhwdBnevAFl_aJ-x3fY62PB3A9VjCrGDZVaA/w200-h200/spirohexane.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<p> The atom 3 is a <a href="http://en.wikipedia.org/wiki/Quaternary_carbon" target="_blank" title="Quaternary carbon in Wikipedia">quaternary carbon</a> while the rest are <a href="http://en.wikipedia.org/wiki/Secondary_carbon" target="_blank" title="Secondary carbon in Wikipedia">secondary carbons</a>. Or, using the <a href="https://metallome.blogspot.com/2021/01/chains-and-rings.html" target="_blank" title="Chains and rings @ this blog">graph theory</a> language, we can say that in the graph <b>(a)</b> the <a href="http://en.wikipedia.org/wiki/Degree_(graph_theory)" target="_blank" title="Degree (graph theory) in Wikipedia"><i>degree</i></a> of vertex 3 is 4 and the degrees of the rest of vertices are 2. The atom 3 is also known as a <i>spiro atom</i> [<a href="#Moss_1999" title="Moss (1999)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/spiro/sp0n1.html#p0" target="_blank" title="Extension and Revision of the Nomenclature for Spiro Compounds, SP-0: Spiro">SP-0</a>] while the whole structure is an example of <a href="http://goldbook.iupac.org/terms/view/S05884" target="_blank" title="spiro union in Gold Book"><i>spiro union</i></a>. </p>
<a name='more'></a>
<p> The structure <b>(a)</b> is named spirohexane or, more systematically, <a href="http://www.chemspider.com/Chemical-Structure.119752.html" target="_blank" title="spiro[2.3]hexane @ ChemSpider">spiro[2.3]hexane</a>. The ‘spiro’ and ‘hexane’ parts, respectively, refer to the spiro union and the fact that <b>(a)</b> contains six carbon atoms<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. The ‘[2.3]’ bit looks very similar to <a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog">von Baeyer</a>’s bridge descriptor, to the degree that the IUPAC recommendations [<a href="#Moss_1999" title="Moss (1999)">1</a>] call it “von Baeyer descriptor”. In fact, it was von Baeyer who proposed the name <i>spirocyclans</i><sup><a href="#Footnote_†" title="Footnote †">†</a></sup> for systems containing two rings which contain one quaternary carbon in common, in the same paper where he first described the nomenclature of bicyclic hydrocarbons [<a href="#Baeyer_1900" title="Baeyer (1900)">2</a>]. However, you’ll notice some important differences between bridge descriptor and spiro descriptor (as I call it; I think it is a bit weird to call the path from point A to point A “a bridge”).</p>
<p> There are two circular paths from vertex 3 back to 3, viz. 3–1–2–3 and 3–4–5–6–3. Just like a bridge descriptor, a spiro descriptor contains the numbers of <i>intervening</i> carbon atoms. So, ‘2’ for 3–1–2–3 and ‘3’ for 3–4–5–6–3, hence ‘[2.3]’ in <b>(a)</b>. Since the minimum number of atoms in a ring is three, a spiro descriptor cannot have either ‘0’ or ‘1’ in it. Also, the numbers are cited from lower to higher, so spiro[2.3]hexane, not <strike>spiro[3.2]hexane</strike>. </p>
<p> You may recall that in von Baeyer names, we number the main (i.e. larger) ring first, starting from one of bridgehead atoms. Well, the numbering of a spiro system is done very differently [<a href="#Moss_1999" title="Moss (1999)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/spiro/sp0n1.html#p12" target="_blank" title="Extension and Revision of the Nomenclature for Spiro Compounds, SP-1.2: Numbering monospiro systems">SP-1.2</a>]:
</p><blockquote> Monospiro hydrocarbons with two monocyclic rings are numbered consecutively starting in the smaller ring at an atom next to the spiro atom, proceeding around the smaller ring back to the spiro atom and then round the second ring. </blockquote>
<p>For me, it does not make any sense. I would give the locant number 1 to the most interesting atom, viz. the spiro atom. </p>
<p> What if there is more than one spiro junction? Consider the structure <b>(b)</b>: </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8qQ3RE7GKDxXo48zvUL3DOw98ZYLGmy_Yy8gK_mr8vM9EHrJcXwUg230tjOLv3Tr1_5qbnr7OygFCrOoyJ2ngDIG3SQ-phFHBgjK0rbQXggGDJPhbAfUju1FpzBgPvgkVJJTXXQ/s600/dispiro.2.0.2.2.octane.png" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="dispiro[2.0.2.2]octane"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8qQ3RE7GKDxXo48zvUL3DOw98ZYLGmy_Yy8gK_mr8vM9EHrJcXwUg230tjOLv3Tr1_5qbnr7OygFCrOoyJ2ngDIG3SQ-phFHBgjK0rbQXggGDJPhbAfUju1FpzBgPvgkVJJTXXQ/w200-h200/dispiro.2.0.2.2.octane.png" width="200" /></a></td></tr>
<tr><th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="2" type="a">
<li> dispiro[2.0.2.2]octane </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Since there are two spiro junctions now, we have to add a multiplier to ‘spiro’, thus ‘dispiro’. The spiro descriptor becomes more complex too. We probably should call it spiro-bridge descriptor, because it contains alternating cycles and bridges: cycle 3–1–2–3 (‘2’), bridge 3–4 (‘0’), cycle 4–5–6–4 (‘2’) and bridge 4–7–8–3 (‘2’), hence <a href="http://www.chemspider.com/Chemical-Structure.124218.html" target="_blank" title="dispiro[2.0.2.2]octane @ ChemSpider">dispiro[2.0.2.2]octane</a>.</p>
<p> More spiro junctions make descriptors messier as now the locants have to be added [<a href="#Moss_1999" title="Moss (1999)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/spiro/sp0n1.html#p14" target="_blank" title="Extension and Revision of the Nomenclature for Spiro Compounds, SP-1.4: Unbranched polyspiro systems">SP-1.4</a>]: </p>
<blockquote> For trispiro and higher spiro systems each time a spiro atom is reached for the second time its locant is cited as a superscript number to the corresponding number of linking atoms. </blockquote>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1SwXv4aLHrN3Suap112QMtWwjufulYjNZy3n_xRVgNYiqiJipDuwva-tJxRalxxvpfBPl2NtsQSNrJsDo9ZrrB0JYOdJtu9ZGvyr8F7JAKkrpkxcpKzUDuH3A-h5hCG9Mj1o9qw/s600/3-rotane.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1SwXv4aLHrN3Suap112QMtWwjufulYjNZy3n_xRVgNYiqiJipDuwva-tJxRalxxvpfBPl2NtsQSNrJsDo9ZrrB0JYOdJtu9ZGvyr8F7JAKkrpkxcpKzUDuH3A-h5hCG9Mj1o9qw/w200-h200/3-rotane.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="3" type="a">
<li> [3]rotane (<a href="http://en.wikipedia.org/wiki/Rotane" target="_blank" title="Rotane in Wikipedia"><i>rotane</i></a>) <br />
trispiro[2.0.2<sup>4</sup>.0.2<sup>7</sup>.0<sup>3</sup>]nonane (<i>spiro</i>) <br />
trispiro[2.0.2.0.2.0]nonane (<i>spiro, CAS index name</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Although <a href="http://www.chemspider.com/Chemical-Structure.124965.html" target="_blank" title="trispiro[2.0.2.0.2.0]nonane @ ChemSpider">trispiro[2.0.2.0.2.0]nonane</a> seems to be a reasonable name for <b>(c)</b>, the preferred IUPAC name would be trispiro[2.0.2<sup>4</sup>.0.2<sup>7</sup>.0<sup>3</sup>]nonane, where ‘2<sup>4</sup>’, ‘2<sup>7</sup>’ and ‘0<sup>3</sup>’ correspond to cycle 4–5–6–4, cycle 7–8–9–7 and bridge 7–3, respectively. </p>
<p> There’s only so much that one can do naming the structures as spiroalkanes. Already in 1911, Dan Rădulescu proposed to name each ring system in a spiro union separately [<a href="#Radulescu_1911" title="Radulescu (1911)">3</a>]. For example, it is obvious that the structure <b>(d)</b> consists of two identical components: </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVPFvM11WseDZiil_2e7XwOYHWrpzelQZD7qtfvnhJZ-viwV6l9OOjxIUnckBLLxVL8vy3Ojb9zsjg139HtAVhFIxL0EhQ2nk2zZR81wzWfrRqWDX80txCHJfmfHyjEUW62qOHVw/s600/9%252C9-spirobifluorene.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVPFvM11WseDZiil_2e7XwOYHWrpzelQZD7qtfvnhJZ-viwV6l9OOjxIUnckBLLxVL8vy3Ojb9zsjg139HtAVhFIxL0EhQ2nk2zZR81wzWfrRqWDX80txCHJfmfHyjEUW62qOHVw/w200-h200/9%252C9-spirobifluorene.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28266" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="fluorene (CHEBI:28266)"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhltSemkbRrALOBXteMeOB6ZsBultvrJhstmzpcWVt1zMqZf2kBEPDrat5sGEhvkzL2Wy0KR_w4G2XI2YAFKjPCVvkwVzf8wIUrjXeI0Z0bz0eZtyLPCXKtK5YrVvAVZi0Oe9z4Wg/w200-h200/fluorene.png" width="200" /></a></td>
</tr>
<tr><th align="center">(d)</th> <th align="center">(e)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="4" type="a">
<li> 9,9′-spirobi[fluorene] (<i>spiro</i>) <br />
9,9′-spirobi[9<i>H</i>-fluorene] (<i>spiro, CAS index name</i>)
</li>
<li> fluorene (<i>trivial, parent hydride, indicated hydrogen omitted</i>) <br />
9<i>H</i>-fluorene (<i>trivial, parent hydride + indicated hydrogen</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> The component <b>(e)</b> is called 9<i>H</i>-fluorene, or simply fluorene. Two components are joined at the position 9. The locants of the second components are primed, therefore the spiro atom is indicated as ‘9,9′’, which is a short way to say “the common atom is found at the position 9 of the first component and the position 9′ of the second component”. The resulting name recommended by IUPAC is <a href="http://www.chemspider.com/Chemical-Structure.119753.html" target="_blank" title="9,9′-spirobifluorene @ ChemSpider">9,9′-spirobi[fluorene]</a>. The CAS name is almost identical except it also contains the <a href="http://goldbook.iupac.org/terms/view/I03004" target="_blank" title="indicated hydrogen in Gold Book">indicated hydrogen</a> within square brackets, thus 9,9′-spirobi[9<i>H</i>-fluorene]. </p>
<p> Can we combine the names of non-dentical ring components in a spiro union? Yes we can. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37915" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="fluoran (CHEBI:37915)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGMXWYFxYHh-ifKevrpkbcxsnn-KECRhPRc2iOLfu7QFj8QlR_P-Vf9lK3O3gib11ovwM49eptG1yO59YUSNSFhMR9n9Sx4gdQEL8M1jGTdUmzInDdCaCNiNWVmrjAydjKaf2-tg/w200-h200/fluoran.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35261" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2-benzofuran (CHEBI:35261)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjr9q_eOolX75j5MT-wsrSJz4KCX78DYVz6RSrrxxx4CBUMijb3qCbQEMSSbTPQ3u6nnf6-6TCMKRty1BSEee5iXaZ14IP8louDP_WN5rM_Shp6XMUOKieikLN2_YHJ_ZOj7MpuSg/w200-h200/2-benzofuran.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:10057" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="9H-xanthene (CHEBI:10057)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsAje6gN7eRF04CsFSjz2D6tW-F57Yq1Jvh70eQMhSa8BJXWa_OkHGbbUEeOamZbnsxOKrQUE_4mQ4-EehLhJ3QTXahWOCIDHmgQuFkss-rASH4HmA-xHMw4oTz4quUrAStIrtSA/w200-h200/9H-xanthene.png" width="200" /></a></td>
</tr>
<tr><th align="center">(f)</th> <th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="6" type="a">
<li> fluoran (<i>trivial</i>) <br />
3<i>H</i>-spiro[2-benzofuran-1,9′-xanthen]-3-one (<i>spiro + substitutive</i>) <br />
spiro[isobenzofuran-1(3<i>H</i>),9′(9′<i>H</i>)-xanthen]-3-one (<i>spiro + substitutive, CAS index name</i>) </li>
<li> 2-benzofuran (<i>fused ring</i>) <br />
isobenzofuran (<i>trivial</i>) </li>
<li> xanthene (<i>trivial, parent hydride, indicated hydrogen omitted</i>) <br />
9<i>H</i>-xanthene (<i>trivial, parent hydride + indicated hydrogen</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> For instance, fluoran <b>(f)</b> — not to be confused with fluorene <b>(e)</b> — is named systemetically as the derivative of a spiro union of <span style="background-color: lightgreen;">2-benzofuran</span> <b>(g)</b> and <span style="background-color: yellow;">xanthene</span> <b>(h)</b>. The spiro atom is found at the position 1 of 2-benzofuran and position 9 of xanthene, thus spiro[<span style="background-color: lightgreen;">2-benzofuran-1</span>,<span style="background-color: yellow;">9′-xanthene</span>]. When the oxo group is added at the position 3 of 2-benzofuran, the whole structure is named as a ketone, i.e. acquires the terminal ‘<span style="background-color: lavender;">one</span>’, with elision of the terminal ‘e’ in ‘xanthene’: 3<i>H</i>-spiro[<span style="background-color: lightgreen;">2-benzofuran-1</span>,<span style="background-color: yellow;">9′-xanthen</span>]-3-<span style="background-color: lavender;">one</span>. IUPAC favours citing indicated hydrogen <i>in front</i> of the complete name, while CAS index names have indicated hydrogen in parentheses <i>after </i>the locants, as in spiro[<span style="background-color: lightgreen;">isobenzofuran-1(3<i>H</i>)</span>,<span style="background-color: yellow;">9′(9′<i>H</i>)-xanthen</span>]-3-<span style="background-color: lavender;">one</span> <sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>. </p>
<p> As you can see, the spiro nomenclature is a jumble of different methods: spiro[<i>x</i>.<i>y</i>]alkane names are a variation on theme of <a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog">von Baeyer names</a>; spiro[<i>component A</i>-<i>locant</i>,<i>locant</i>′-<i>component B</i>] names are built in the fashion of <a href="http://metallome.blogspot.com/2021/05/fused-ring-names.html" target="_blank" title="Fused ring names @ this blog">fused ring names</a>; and the spirobi[<i>component</i>] names are very much like identical-ring assembly names. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> The name ‘spirohexane’, as well as that of the simpler (and the simplest possible) spiro structure, <a href="http://www.chemspider.com/Chemical-Structure.8734.html" target="_blank" title="spiropentane @ ChemSpider">spiropentane</a>, does not really need a descriptor because there is only one way to construct a spiro union containing six (or five) carbon atoms. Similarly, von Baeyer descriptor ‘[1.1.0]’ in <a href="http://www.chemspider.com/Chemical-Structure.119751.html" target="_blank" title="bicyclo[1.1.0]butane @ ChemSpider">bicyclo[1.1.0]butane</a> is redundant, as ‘bicyclobutane’ is unambiguous. </td></tr>
<tr><td valign="top">†</td>
<td> To quote: “Welche ein beiden Ringen gemeinschaftliches quaternäres Kohlenstoffatom enthalten: Spirocyclane, von »spira« die Brezel” (That <where> both rings contain a common quaternary carbon atom: spirocyclans, from <a href="http://en.wiktionary.org/wiki/spira#Latin" target="_blank" title="spira in Wiktionary"><i>spira</i></a> “the pretzel”) [<a href="#Baeyer_1900" title="Baeyer (1900)">2</a>]. </td></tr>
<tr><td valign="top">‡</td>
<td> Somewhat confusingly, indicated hydrogens are there <i>not</i> to indicate the presence of actual hydrogen atoms but to fix the positions of double bonds in <a href="http://metallome.blogspot.com/2021/03/mancude-rings-and-annulenes.html" target="_blank" title="Mancude rings and annulenes @ this blog">mancude systems</a>. For instance, in spiro[isobenzofuran-1(3<i>H</i>),9′(9′<i>H</i>)-xanthen]-3-one <b>(f)</b> neither position 3 nor 9′ has any hydrogen atoms attached. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Moss_1999"></a>
<li> Moss, G.P. (1999) Extension and revision of the nomenclature for spiro compounds (IUPAC Recommendations 1999). <a href="http://doi.org/10.1351/pac199971030531" target="_blank" title="Moss (1999) Pure Appl. Chem. 71, 531-558."><i>Pure and Applied Chemistry</i> <b>71</b>, 531—558</a>. </li>
<a name="Baeyer_1900"></a>
<li> Baeyer, A. (1900) Systematik und Nomenclatur bicyclischer Kohienwasserstoffe. <a href="http://doi.org/10.1002/cber.190003303187" target="_blank" title="Baeyer (1900) Ber. Dtsch. Chem. Ges. 33, 3771-3775."><i>Berichte der Deutschen Chemischen Gesellschaft</i> <b>33</b>, 3771—3775</a>. </li>
<a name="Radulescu_1911"></a>
<li> Radulescu, D. (1911) Über die Nomenklatur der Spirane. <a href="http://doi.org/10.1002/cber.191104401152" target="_blank" title="Radulescu (1911) Ber. Dtsch. Chem. Ges. 44, 1023-1026."><i>Berichte der Deutschen Chemischen Gesellschaft</i> <b>44</b>, 1023—1026</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-14828836901243323482021-05-30T18:00:00.067+01:002023-08-07T09:57:56.976+01:00Fused ring names<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35559" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="furan (CHEBI:35559)"><img border="0" data-original-height="800" data-original-width="800" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6o42pnEa6xOKs6ZKJi7lloul6UO5VesjFfzGQjrVhEa3XNzVj9bg8wzqYnEutZ3zKAweX1fKDY0aqdMfcwwbiiGIB5YdvIiPi1Re6NkElfhjjX4Sb1UvzYdeN_DxZS1YjxJW4lw/w200-h200/furan.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="1" type="a">
<li> furan (<i>trivial, retained</i>) <br />
oxole (<a href="http://metallome.blogspot.com/2021/04/hantzsch-widman-names.html" target="_blank" title="Hantzsch-Widman names @ this blog"><i>Hantzsch-Widman</i></a>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Knowing that the structure <b>(a)</b> is called <a href="http://metallome.blogspot.com/p/monoheterocyclic-parent-hydrides.html" target="_blank" title="Monoheterocyclic parent hydrides @ this blog">furan</a>, let’s name the structure <b>(b)</b>.</p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:34890" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2-nitrofuran (CHEBI:34890)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjO7qscQoeloKwByA-r6A2BZYuPyCKzDFxrbpXaSCITVT7Mq7hjItu-w21pVzAVBpdVO8kjE01KR084Vf96ffJ9E1A-UF0wFpNPkfFuIag5LyYnDqAJWQq4x_RQdbAIgpMKEDPYEQ/w200-h200/2-nitrofuran.png" width="200" /></a></td></tr>
<tr><th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="2" type="a">
<li> 2-nitrofuran (<i>substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Easy: 2-nitrofuran. </p>
<p> Keeping that in mind, what kind of structure do you think corresponds to the name ‘2-benzofuran’?</p>
<a name='more'></a>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35261" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2-benzofuran (CHEBI:35261)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcSX5af9JdC04kpjpO7z3Jgi0yr2-_2lGZBTyw3LTG3edBLIfaFrg7pGdAWnMgKS9CgsRNOYV2FK6Z9V_aLeVcDcVAiUWcluajoED1sKseB8Qw78E7_Vv0XUqmi_wzJcFFgErKTA/w200-h200/2-benzofuran.png" width="200" /></a></td> </tr>
<tr><th align="center">(c)</th></tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="3" type="a">
<li> 2-benzofuran (<i>fused ring</i>) <br />
benzo[<i>c</i>]furan (<i>fused ring</i>) <br />
isobenzofuran (<i>trivial</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Not so easy now, eh? Although the names ‘2-<span style="background-color: lavender;">nitro</span><span style="background-color: yellow;">furan</span>’ and ‘2-<span style="background-color: palegreen;">benzo</span><span style="background-color: yellow;">furan</span>’ look similar, they are built according to very different principles. While the former is a simple <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">substitutive name</a> — meaning that one hydrogen atom of <span style="background-color: yellow;">furan</span> <b>(a)</b> is substituted at the position 2 by a <span style="background-color: lavender;">nitro</span> group — the latter is a <i>fused ring</i> name. In 2-benzofuran <b>(c)</b>, the benzene ring is not a substituent; rather, it is <i>fused</i> to the furan ring. According to the IUPAC recommendations [<a href="#Moss_1998" title="Moss (1998)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/fusedring/FR1.html#111" target="_blank" title="Fused Ring Nomenclature, FR-1.1.1: Ortho-fused">FR-1.1.1</a>], the two rings are called fused (or <i>ortho</i>-fused) when they have two atoms and one bond in common. A fused ring name is built of a “parent component”, for instance ‘<span style="background-color: yellow;">furan</span>’, and a “fusion prefix” (in fact a combining form), e.g. ‘<span style="background-color: palegreen;">benzo</span>’.</p>
<p> What about the ‘2’ in ‘2-benzofuran’? IUPAC refer to this number as a locant [<a href="#Moss_1998" title="Moss (1998)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/fusedring/FR22.html#228" target="_blank" title="Fused Ring Nomenclature, FR-2.2.8: Heterobicyclic components with a benzene ring">FR-2.2.8</a>]:</p>
<blockquote> The locants quoted correspond to the numbering of the bicyclic structure, which follows <a href="http://www.qmul.ac.uk/sbcs/iupac/fusedring/FR53.html#54" target="_blank" title="Fused Ring Nomenclature, FR-5.4: Order of preference between alternative numbering systems">FR-5.4</a>. </blockquote>
<p> Have a look at the numbering of <b>(c)</b> according to the aforementioned rule: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35261" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2-benzofuran (CHEBI:35261)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjr9q_eOolX75j5MT-wsrSJz4KCX78DYVz6RSrrxxx4CBUMijb3qCbQEMSSbTPQ3u6nnf6-6TCMKRty1BSEee5iXaZ14IP8louDP_WN5rM_Shp6XMUOKieikLN2_YHJ_ZOj7MpuSg/w200-h200/2-benzofuran.png" width="200" /></a></td> </tr>
<tr><th align="center">(c)</th></tr>
</table>
</center>
<p> What we see is that the oxygen atom in 2-benzofuran is found at the position 2, as opposed to the oxygen atom in 1-benzofuran which is found at the position 1: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35260" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1-benzofuran (CHEBI:35260)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPdAokUPEYO90YQwW4nFyXF7Z4J-oH4ODUFPyWgtSjDDIlvYAltrpU9FrfdyAE_U7975Qw8xLBUM1C9WXXV_zAI1a92oQEi3v7u8W4meGBpn3SIEcvn4x_CeHEPNFvSg1ak-meVw/w200-h200/1-benzofuran.png" width="200" /></a></td> </tr>
<tr><th align="center">(d)</th></tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="4" type="a">
<li> 1-benzofuran (<i>fused ring</i>) <br />
benzo[<i>b</i>]furan (<i>fused ring</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> As you can see, the use of locant numbers here is quite unlike to that of substitutive nomenclature. ‘2’ in ‘2-benzofuran’ does not tell us to which atoms of furan ring the benzene ring is fused. It tells us <i>indirectly</i> that the rings should be fused in such a way that furan’s oxygen atom would find itself at the position 2. </p>
<p> An alternative method is to use italic letters <i>a</i>, <i>b</i>, <i>c</i>, etc. for the <i>sides</i> of the parent ring [<a href="#Moss_1998" title="Moss (1998)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/fusedring/FR41.html#41" target="_blank" title="Fused Ring Nomenclature, FR-4.1: Identification of sides of parent components">FR-4.1</a>]. Thus, the side (1,2) is <i>a</i>; the side (2,3) is <i>b</i>, etc.<sup><a href="#Footnote_*" title="Footnote *">*</a></sup> For naming purposes, these “letter locants” imply <i>directionality</i>. In case of furan, the side <i>a</i> (1,2) is <i>not</i> equivalent to the side <i>e</i> (5,1) and the side <i>b</i> (2,3) is <i>not</i> equivalent to the side <i>d</i> (4,5): </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOoVv_q0SFfl5KaOmpWytdR9tOhccWwtMYLJRDITx1Z6dVt-eE5cn6kmTdqS0q7rVIWc5XLV_iKMmX5OgEXE0SM_VDuqyBg98sX4W1-YlEJkg1Tp6sFW8Hp4TpY0AaR9g91vGK2A/s800/furan.png" style="display: block; padding: 1em 0px; text-align: center;"><img alt="" border="0" data-original-height="800" data-original-width="800" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOoVv_q0SFfl5KaOmpWytdR9tOhccWwtMYLJRDITx1Z6dVt-eE5cn6kmTdqS0q7rVIWc5XLV_iKMmX5OgEXE0SM_VDuqyBg98sX4W1-YlEJkg1Tp6sFW8Hp4TpY0AaR9g91vGK2A/w200-h200/furan.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<p> Thus the structures <b>(c)</b> and <b>(d)</b> can be called benzo[<i>c</i>]furan and benzo[<i>b</i>]furan<sup><a href="#Footnote_†" title="Footnote †">†</a></sup>, respectively. The bit in square brackets is referred to as “fusion descriptor” [<a href="#Hellwich_2020" title="Hellwich et al. (2020)">2</a>]. </p>
<p> In fact this latter naming method is preferred by IUPAC for the structures like <b>(e)</b> and <b>(f)</b>: </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47802" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="5H-dibenzo[b,f]azepine (CHEBI:47802)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgpXTro5xcggHOjUweADt0r7Py9YrAkYcgHyXdCBosR46CtPFM1nIE8vQ6qezSDs4mRCegv0wM5C1k-q7TuoaTR766V4nhVtJmvdsjwx3f4-p40VYYs1MrDAvck4CWCyTYn3b-MdA/s0/dibenzazepine.png" /></a></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:358732" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="dibenzo-18-crown-6 (CHEBI:358732)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhA086evBqxCf8hDIWHPUPIKn2RdgTDf9yTdGS1zoY2DxZkQBTIBEawNGCnSIYBWTiNjkGl1v54OS1Cc69N3GC7_qoaqdz-xRu3PfKgWpx1RvVGTNMxRyQO3ZWJltpV9IUmpbaA6Q/w200-h200/dibenzo-18-crown-6.png" width="200" /></a></td></tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="5" type="a">
<li> 5<i>H</i>-dibenzo[<i>b</i>,<i>f</i>]azepine (<i>Hantzsch-Widman + fused ring</i>) </li>
<li> dibenzo[<i>b</i>,<i>k</i>][1,4,7,10,13,16]hexaoxacyclooctadecane<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup> (<i>replacement + fused ring</i>) <br />
dibenzo-18-crown-6 (<a href="http://metallome.blogspot.com/2021/04/many-names-of-crowns.html" target="_blank" title="The many names of crowns @ this blog"><i>Pedersen</i></a>) </li>
</ol>
</td>
</tr>
</table>
</center><p> For more complex fused ring systems, combinations of numerical and letter locants are employed. Consider the structure <b>(g)</b>.</p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36708" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1H-imidazo[4,5-c]quinoline (CHEBI:36708)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcEoe7bzvwhSOgX31T3fFWNTKrOg3n1DefiBpjkRVvOzZyDzAmFQcGDvRVz8y-HNZ5wYnJNvIy6WIueR5sG8y0dlym3OfjdOu8GC3VTkWicphcyOx20ypbTnh2yLawDUOEaccpKQ/w200-h200/1H-imidazo%255B4%252C5-c%255Dquinoline.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16069" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1H-imidazole (CHEBI:16069)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzF_nuLCDVNucUQhQ8o5OGYAiTrD6eyEv4Rq5epVmVz4U_rvB0bkE51F0qtZBDQfT_jvijnFkie6bv3WmEEoIgZpVzRMJj4NX_lXKDt-FrtPXXud97p4iSvb6h0Ui5pxRVO50zfw/s200/1H-imidazole.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17362" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="quinoline (CHEBI:17362)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHy5CfCI9fruocsOBtpgj-KOAc58gf_9Y0KsKsKym0fkXqIArkTFwk6Qy_nmjoKSuYJuMtdxKIA_Qp0u51a5sCv0Xf8ZAx03GMTciYEdlWb6fY9oYO8BNJltRnWW1-S3S5Ketkpg/s1600/quinoline.png" /></a></td>
</tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th> <th align="center">(i)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="7" type="a">
<li> 1<i>H</i>-imidazo[4,5-<i>c</i>]quinoline (<i>fused ring</i>) </li>
<li> 1<i>H</i>-imidazole (<i>trivial, parent hydride</i>) </li>
<li> quinoline (<i>trivial, parent hydride</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> It could be described as a fusion of 1<i>H</i>-imidazole <b>(h)</b> and quinoline <b>(i)</b>. More specifically, the atoms <span style="background-color: palegreen;">4</span> and <span style="background-color: palegreen;">5</span> of <span style="background-color: palegreen;">1<i>H</i>-imidazole</span> are fused with the atoms 3 and 4 (aka side <span style="background-color: yellow;"><i>c</i></span>) of <span style="background-color: yellow;">quinoline</span>, respectively. The resulting name is <span style="background-color: palegreen;">1<i>H</i>-imidazo</span>[<span style="background-color: palegreen;">4,5</span>-<span style="background-color: yellow;"><i>c</i></span>]<span style="background-color: yellow;">quinoline</span>, where ‘[4,5-<i>c</i>]’ is a fusion descriptor. </p>
<p> You might have noticed that I am not a big fan of locants. In my view, the fewer locants the name has the better. And fused ring names provide excellent examples to illustrate my point. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27616" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="psoralen (CHEBI:27616)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEglsVY6p4ZcZ7o7_j-UBxP8lN0H7aOeP4R0Q2wUfda9pLKc64LXIcPR6rw6MlviI1pcXb4tcSkp1WSoHqMmhVNbyyfEkkvoK35QmuBZLpmV6mEDWBH_yZtDGG6ahUXf4XmL5uNisg/w200-h200/psoralen.png" width="200" /></a></td> </tr>
<tr><th align="center">(j)</th></tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="10" type="a">
<li> psoralen (<i>trivial</i>) <br />
7<i>H</i>-furo[3,2-<i>g</i>]chromen-7-one (<i>fused ring</i>) <br />
7<i>H</i>-furo[3,2-<i>g</i>][1]benzopyran-7-one<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup> (<i>fused ring</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> To name <b>(j)</b> systematically, we first take furan <b>(a)</b> and fuse it with 2<i>H</i>-chromene <b>(k)</b>:</p><center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35601" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="2H-chromene (CHEBI:35601)"><img border="0" data-original-height="800" data-original-width="800" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjy9OcDu1efbCvgrDHxQpTOLb6DZNGizSGRNGxaRDSau_RSGPa1x_Sfu39L9ze7BX0IHjXeAwA0bU0o-X985q9OjaVJmK6lkVHcCIsQPrIIv8HpkOKuuw1zweSai2HXLG-yaNHoaA/w200-h200/chromene.png" width="200" /></a></td> </tr>
<tr><th align="center">(k)</th></tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="11" type="a">
<li> 2<i>H</i>-chromene (<i>trivial, parent hydride</i>) <br />
2<i>H</i>-1-benzopyran (<i>fused ring</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> More specifically, the atoms <span style="background-color: palegreen;">3</span> and <span style="background-color: palegreen;">2</span> of <span style="background-color: palegreen;">furan</span> are fused with the atoms 6 and 7 (aka side <span style="background-color: yellow;"><i>g</i></span>) of <span style="background-color: yellow;">chromene</span>, respectively. [Alternatively, we can use the systematic name 2<i>H</i>-<span style="background-color: yellow;">1-benzopyran</span> instead of chromene; here, the locant ‘1’ refers to the numbering of the oxygen atom, in the same fashion we’ve seen in 1-benzofuran <b>(d)</b>.] However, once it is done, the whole skeleton gets <i>renumbered</i> according to the rule <a href="http://www.qmul.ac.uk/sbcs/iupac/fusedring/FR53.html#54" target="_blank" title="Fused Ring Nomenclature, FR-5.4: Order of preference between alternative numbering systems">FR-5.4</a>. And so, the chromene position 2 becomes the new position 7, and the oxo group is added to this new position, hence ‘7<i>H</i>-<span style="background-color: palegreen;">furo</span>[<span style="background-color: palegreen;">3,2</span>-<span style="background-color: yellow;"><i>g</i></span>]<span style="background-color: yellow;">chromen</span>-7-one’ (or ‘7<i>H</i>-<span style="background-color: palegreen;">furo</span>[<span style="background-color: palegreen;">3,2</span>-<span style="background-color: yellow;"><i>g</i></span>]<span style="background-color: yellow;">[1]benzopyran</span>-7-one’<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>).</p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEs8tsJ-cya12i7HuV-LWKOEK-TxrLgL9wdKk0VxTajkxmnsFpGDwroOgqGieGikrniSRcQOBtEu5vLZthNabWabohmsSEDrVktdj2QhRrWe9a0JzZAM9PU9-7IirclQbM5EbaTQ/s800/psoralen.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="800" data-original-width="800" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEs8tsJ-cya12i7HuV-LWKOEK-TxrLgL9wdKk0VxTajkxmnsFpGDwroOgqGieGikrniSRcQOBtEu5vLZthNabWabohmsSEDrVktdj2QhRrWe9a0JzZAM9PU9-7IirclQbM5EbaTQ/w200-h200/psoralen.png" width="200" /></a></td> </tr>
<tr><th align="center">(j)</th></tr>
</table>
</center>
<p> Names constructed thus contain locants meaning disparate things. But we shouldn’t let this relatively minor annoyance obscure the big picture. Stripped of locants, the systematic name ‘furochromenone’ or, even more informatively, ‘furobenzopyranone’, already gives us much better idea of the structure <b>(j)</b> than its trivial name, ‘psoralen’. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> What happens if there are more than 26 sides? Then the additional sides are marked as <i>a</i><sub>1</sub>, <i>b</i><sub>1</sub>, <i>c</i><sub>1</sub> and so on, then <i>a</i><sub>2</sub>, <i>b</i><sub>2</sub>, <i>c</i><sub>2</sub>, etc. [<a href="#Moss_1998" title="Moss (1998)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/fusedring/FR41.html#41" target="_blank" title="Fused Ring Nomenclature, FR-4.1: Identification of sides of parent components">FR-4.1</a>]. No, it’s not elegant; hopefully, I’ll never use letter locants like these. </td>
</tr>
<tr><td valign="top">†</td>
<td> The lower locants are preferred, so benzo[<i>b</i>]furan is preferred to benzo[<i>d</i>]furan. </td></tr>
<tr><td valign="top">‡</td>
<td> The IUPAC recommends to use square brackets around the locants thus [<a href="#Moss_1998" title="Moss (1998)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/fusedring/FR46.html#48" target="_blank" title="Fused Ring Nomenclature, FR-4.8: Heteroatom locants of components">FR-4.8</a>]:
<blockquote> When a component requires the citation of locants (<i>e.g.</i> in a Hantzsch-Widman name) these are always quoted in square brackets. Note that these numbers in brackets only refer to the numbering of the component and have no significance in the final numbering of the complete fused ring system. </blockquote>
Why the locants which are “free” in parent component names (such as 1,4,7,10,13,16-hexaoxacyclooctadecane) should be put in square brackets in fused ring names (e.g. dibenzo[<i>b</i>,<i>k</i>][1,4,7,10,13,16]hexaoxacyclooctadecane) is not exactly clear.
</td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Moss_1998"></a>
<li> Moss, G.P. (1998) Nomenclature of fused and bridged fused ring systems (IUPAC Recommendations 1998). <a href="http://doi.org/10.1351/pac199870010143" target="_blank" title="Moss (1998) Pure Appl. Chem. 70, 143-216."><i>Pure and Applied Chemistry</i> <b>70</b>, 143—216</a>. </li>
<a name="Hellwich_2020"></a>
<li> Hellwich, K.-H., Hartshorn, R.M., Yerin, A., Damhus, T. and Hutton, A.T. (2020). Brief guide to the nomenclature of organic chemistry (IUPAC Technical Report). <a href="http://doi.org/10.1515/pac-2019-0104" target="_blank" title="Hellwich et al. (2020) Pure Appl. Chem. 92, 527-539."><i>Pure and Applied Chemistry</i> <b>92</b>, 527—539</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-84085735316689591272021-05-14T23:00:00.041+01:002023-08-07T09:59:08.210+01:00von Baeyer names<p> Here’s a cute little structure: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49287" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="housane (CHEBI:49287)"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgKWSz8dNHt8BH2Ht47BCSfBe57ux19ExwkJLgVZ4k-3GdvaDOZpD82678HqwIYRuiPdPBLvaIZXfxiLlq6M_vHv24l2ij4b-uQ82HrghHOCjH8qLwk6aHrrSkMjnQj_FG4YIfI5g/w200-h200/housane.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr></table>
</center>
<center>
<table>
<tr><td><ol start="1" type="a">
<li> housane (<i>trivial</i>) <br />
bicyclo[2.1.0]pentane (<i>von Baeyer</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Drawn like this, <b>(a)</b> looks like a little house and, indeed, is known as a housane. Alexander Senning called this structure “the poor man’s housane” [<a href="#Senning_2019" title="Senning (2019)">1</a>, p. 77] while referring to <a href="http://pubchem.ncbi.nlm.nih.gov/compound/138295" target="_blank" title="Pentaprismane @ PubChem">pentaprismane</a> as “the rich man’s housane” [<a href="#Senning_2019" title="Senning (2019)">1</a>, p. 78]. Of course, there is a systematic name too. <a name='more'></a> To arrive to it, we need to get acquainted with a naming system known as <a href="http://en.wikipedia.org/wiki/Von_Baeyer_nomenclature" target="_blank" title="Von Baeyer nomenclature in Wikipedia">von Baeyer nomenclature</a>. The method of naming of bicyclic hydrocarbons was described by <a href="http://en.wikipedia.org/wiki/Adolf_von_Baeyer" target="_blank" title="Adolf von Baeyer in Wikipedia">Adolf von Baeyer</a> in 1900 [<a href="#Baeyer_1900" title="Baeyer (1900)">2</a>]. </p>
<p> First, let’s number the carbon atoms thus: </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNk3VGqj3GbFrgHEMjiCSe28zA7jQsg0PJAMsomKUBhoePkhRoDp_G3dX6ZRdduPsbum0EHNHDhdf_4aitXrfzOK1RePRT4gDKo3tkRgfmZjSya3OSCzwBOHqFl8TybpTDz9LGrQ/s600/housane.jpg" style="margin-left: 1em; margin-right: 1em;" title="housane numbering"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNk3VGqj3GbFrgHEMjiCSe28zA7jQsg0PJAMsomKUBhoePkhRoDp_G3dX6ZRdduPsbum0EHNHDhdf_4aitXrfzOK1RePRT4gDKo3tkRgfmZjSya3OSCzwBOHqFl8TybpTDz9LGrQ/w200-h200/housane.jpg" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<p> Note that the atoms 1 and 4 are <a href="http://en.wikipedia.org/wiki/Tertiary_carbon" target="_blank" title="Tertiary carbon in Wikipedia">tertiary carbon atoms</a> while the atoms 2, 3 and 5 are <a href="http://en.wikipedia.org/wiki/Secondary_carbon" target="_blank" title="Secondary carbon in Wikipedia">secondary carbons</a>. Or, using the <a href="https://metallome.blogspot.com/2021/01/chains-and-rings.html" target="_blank" title="Chains and rings @ this blog">graph theory</a> language, we can say that in the graph <b>(a)</b> the <a href="http://en.wikipedia.org/wiki/Degree_(graph_theory)" target="_blank" title="Degree (graph theory) in Wikipedia"><i>degrees</i></a> of vertices 1 and 4 are 3 while the degrees of the rest of vertices are 2. </p>
<p> There are three possible paths between the vertices 1 and 4, viz. 1–4; 1–5–4; and 1–2–3–4. von Baeyer called these paths <i>Brücken</i> (“bridges”) and assigned them the numbers corresponding to the numbers of intervening carbon atoms. Thus, ‘0’ for the direct link 1–4; ‘1’ for 1–5–4; and ‘2’ for 1–2–3–4. von Baeyer referred to these three numbers as “characteristic”. Modern IUPACese employs the word <a href="http://goldbook.iupac.org/terms/view/B00736" target="_blank" title="bridge in Gold Book"><i>bridge</i></a> in von Baeyer sense while the tertiary carbon atoms connected by the bridge are called <i>bridgeheads</i><sup><a href="#Footnote_*" title="Footnote *">*</a></sup> [<a href="#Moss_1999" title="Moss (1999)">3</a>].</p>
<p> Next, von Baeyer suggested to name a bicyclic saturated hydrocarbon containing <i>n</i> carbon atoms ‘bicyclo<i>n</i>ane’. Thus <b>(a)</b> is ‘bicyclopentane’. Finally, this name is combined with characteristic numbers, thus yielding ‘bicyclo-[0,1,2]-pentane’. </p>
<p> The modern version of von Baeyer system cites the characteristic numbers in the reverse order to that of the original paper by von Baeyer (that is, from the highest to the lowest), separates them by full stops, and does not use the dashes; the [<i>x</i>.<i>y</i>.<i>z</i>] bit is referred to as “bridge descriptor” [<a href="#Hellwich_2020" title="Hellwich et al. (2020)">4</a>]. So the modern systematic name of <b>(a)</b> would be ‘bicyclo[2.1.0]pentane’. However, these differences are not important. You can arrive to the structure <b>(a)</b> no matter what is the order of citation in the bridge descriptor. For all I know, it could be [1.2.0] or [2.0.1]. Nor should we worry about numbering of the atoms because no locants enter the systematic name. </p>
<p> The situation gets more complicated when we move to the bridged systems with three or more rings. The original von Baeyer method was extended to tricyclic systems by Buchner and Weigand [<a href="#Buchner_&_Weigand_1913" title="Buchner & Weigand (1913)">5</a>] and further developed by IUPAC [<a href="#Moss_1999" title="Moss (1999)">3</a> and references therein]. Consider the structure <b>(b)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:40519" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="adamantane (CHEBI:40519)"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjXTwzU9CGfsUrOh_h79TagCVvgNDQZGagTis7DqdO0yZmUgYt5poAGUuC2blSpg6xUiY-GkjC3psWuC4_XQO3QDGcQKyle_YvkN3aGEUvJOxq-F4DGO3McvXAKvF91ZvX-2VYOHQ/w200-h200/adamantane.png" width="200" /></a></td></tr>
<tr><th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="2" type="a">
<li> adamantane (<i>trivial, parent hydride</i>) <br />
tricyclo[3.3.1.1<sup>3,7</sup>]decane (<i>von Baeyer</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> We need to number the atoms again, but this time the way we do it is important. First, we have to identify the <i>main ring</i> thus [<a href="#Moss_1999" title="Moss (1999)">3</a>]: </p>
<blockquote> The main ring is selected so as to include as many skeletal atoms of the polycyclic compound as possible. </blockquote>
<p> After that, we number the atoms </p>
<blockquote>from a bridgehead atom via the longest path to the second bridgehead atom; numbering of atoms continues round the main ring; and then the main bridge atoms are numbered starting from the lower numbered bridgehead atom. </blockquote>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgGNoQdazKr1liVGJraZlxKtkowtar_hQrmFMHSKmpxcvURXY4TIHAqQhCPLDodbg9kASKaX8rZyAC4iZJNYaiWM-L0l9yEJCUY8PibU-uV7ba7r9tIjYlQrgyQSppHmNi-HUFdw/s600/adamantane.jpg" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="adamantane numbering"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgGNoQdazKr1liVGJraZlxKtkowtar_hQrmFMHSKmpxcvURXY4TIHAqQhCPLDodbg9kASKaX8rZyAC4iZJNYaiWM-L0l9yEJCUY8PibU-uV7ba7r9tIjYlQrgyQSppHmNi-HUFdw/w200-h200/adamantane.jpg" width="200" /></a></td></tr>
<tr><th align="center">(b)</th>
</tr>
</table>
</center>
<p> The main ring is 1–2–3–4–5–6–7–8–1. Between the two bridgehead atoms 1 and 5 there are three bridges: 1–2–3–4–5 (‘3’), 5–6–7–8–1 (also ‘3’) and 1–9–5 (‘1’). Fair enough. But then there is another bridge between 3–10–7 (also ‘1’). For this second bridge, we have to indicate its bridgehead atoms. To do that, we use the superscript locants ‘3,7’, which explains why do we need a particular numbering order. The complete bridge descriptor is ‘[3.3.1.1<sup>3,7</sup>]’. Since the structure contains three cycles and ten carbon atoms, its full name is ‘tricyclo[3.3.1.1<sup>3,7</sup>]decane’. </p>
<p> Compared with alkanes and cycloakanes, von Baeyer names do not immediately bring to mind the corresponding structures. Even the simplest von Baeyer name will make you reach for pen and paper. Another problem is pronounceability. Try saying pentane, cyclopentane and bicyclo[2.1.0]pentane aloud and you’ll know what I mean. The names like tricyclo[3.3.1.1<sup>3,7</sup>]decane are worse still since now the bridge descriptor contains two (semantically different!) kinds of numbers. It never was a good idea, if you ask me, and it shouldn’t come as a surprise that in many databases these numbers got jumbled together, as in ‘tricyclo[3.3.1.13,7]decane’. </p>
<p> To name heteropolycyclic molecules such as <b>(c)</b>, we can combine von Baeyer system with <a href="http://metallome.blogspot.com/2020/06/skeletal-replacement-nomenclature.html" target="_blank" title="Skeletal replacement nomenclature @ this blog">skeletal replacement</a>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:6824" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="hexamethylenetetramine (CHEBI:6824)"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjPRKJ6k-W0pwhWZN4YS88BA3Zz6kgoDK3Es1Bs5b9RCto5NJgdjDgMEIfPtEUXAAp8ylfxaEX4Fp77WJ3y0Pc-_qG4Cesgufs5Y4y2rqYo0VKJjeK2kv9ccq0sg5a95K3c-21gQ/w200-h200/hexamethylenetetramine.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="3" type="a">
<li> methenamine (<i>INN</i>) <br />
1,3,5,7-tetraazaadamantane (<i>trivial + replacement</i>) <br />
1,3,5,7-tetraazatricyclo[3.3.1.1<sup>3,7</sup>]decane (<i>von Baeyer + replacement</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<p> Continuing in this fashion, von Baeyer system could be taken to ridiculous heights, such as 2,4,6,8,9,10-hexaoxa-1,3,5,7-tetrasilatricyclo[3.3.1.1<sup>3,7</sup>]decane for <b>(d)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51170" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tetrasilsesquioxane cage (CHEBI:51170)"><img border="0" data-original-height="600" data-original-width="600" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWeVWC5J4elaJ2lpGGMMxZNPAeUVcucmqJbS46wNjSFpejBbDjI5EjuelxGhm6-QQFNYawbwlk0C4IJChJvy6rw1bqdx2MgMAM4u5AlCvr8s5_3a8CECVy75IVNMRFD2hktgdsUQ/w200-h200/tetrasilsesquioxane_cage.png" width="200" /></a></td></tr>
<tr><th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="4" type="a">
<li> 2,4,6,8,9,10-hexaoxa-1,3,5,7-tetrasilatricyclo[3.3.1.1<sup>3,7</sup>]decane (<i>von Baeyer + replacement</i>) <br />
tricyclo[3.3.1.1<sup>3,7</sup>]tetrasiloxane (<i>von Baeyer for ring systems consisting of repeating units</i>) <br /></li>
</ol>
</td>
</tr>
</table>
</center>
<p> Alternatively, the same structure could be given a much shorter name, tricyclo[3.3.1.1<sup>3,7</sup>]tetrasiloxane, using the method “for ring systems consisting of repeating units” [<a href="#Red_Book_2005" title="Red Book (2005)">6</a>, p. 100]. </p>
<a name="Footnote_*"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> “Bridgehead” is an English calque of the French military term <a href="http://en.wiktionary.org/wiki/t%C3%AAte_de_pont" target="_blank" title="tête de pont in Wiktionary"><i>tête de pont</i></a>. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Senning_2019"></a>
<li> Senning, A. <a href="http://doi.org/10.1515/9783110612714" target="_blank" title="Senning (2019) The Etymology of Chemical Names."><i>The Etymology of Chemical Names: Tradition and Convenience vs. Rationality in Chemical Nomenclature</i></a>. De Gruyter, Berlin—Boston, 2019. </li>
<a name="Baeyer_1900"></a>
<li> Baeyer, A. (1900) Systematik und Nomenclatur bicyclischer Kohienwasserstoffe. <a href="http://doi.org/10.1002/cber.190003303187" target="_blank" title="Baeyer (1900) Ber. Dtsch. Chem. Ges. 33, 3771-3775."><i>Berichte der Deutschen Chemischen Gesellschaft</i> <b>33</b>, 3771—3775</a>. </li>
<a name="Moss_1999"></a>
<li> Moss, G.P. (1999) Extension and revision of the von Baeyer system for naming polycyclic compounds (including bicyclic compounds) (IUPAC Recommendations 1999). <a href="http://doi.org/10.1351/pac199971030513" target="_blank" title="Moss (1999) Pure Appl. Chem. 71, 513-529."><i>Pure and Applied Chemistry</i> <b>71</b>, 513—529</a>. </li>
<a name="Hellwich_2020"></a>
<li> Hellwich, K.-H., Hartshorn, R.M., Yerin, A., Damhus, T. and Hutton, A.T. (2020). Brief guide to the nomenclature of organic chemistry (IUPAC Technical Report). <a href="http://doi.org/10.1515/pac-2019-0104" target="_blank" title="Hellwich et al. (2020) Pure Appl. Chem. 92, 527-539."><i>Pure and Applied Chemistry</i> <b>92</b>, 527—539</a>.
<a name="Buchner_&_Weigand_1913"></a>
</li><li> Buchner, E. and Weigand, W. (1913) Bornylen und Diazoessigester. [Nebst einer Nomenklatur tricyclischer Kohlenstoff‐Ringsysteme nach Adolf von Baeyer]. <a href="http://doi.org/10.1002/cber.191304602130" target="_blank" title="Buchner & Weigand (1913) Ber. Dtsch. Chem. Ges. 46, 2108-2117."><i>Berichte der Deutschen Chemischen Gesellschaft</i> <b>46</b>, 2108—2117</a>. </li>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-91695953893438622652021-05-05T00:00:00.032+01:002022-02-03T11:52:33.862+00:00Bicycles<p> How many rings has the structure <b>(a)</b>? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:39258" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="diphenyl ether (CHEBI:39258)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUtrsmvJYj-7MAcwYGhQdk6oGvR1TN91myVpUFC3O8pIiELgocg81dNLFDEzY7g2ra5iYVUJnns2b49GIfv9s_Trt5JniWplvU_ANMzfV59N7gNg52v8MI7wBRI6Aks7XJI0ASiw/s200/diphenyl_ether.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="1" type="a">
<li> diphenyl ether (<i>functional class</i>) <br />
1,1′-oxydibenzene (<i>multiplicative</i>) <br />
phenoxybenzene (<i>substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Why, there are two, you’ll say. Anybody can see that. And you’ll be right. </p>
<p> What about <b>(b)</b> then? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:71546" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="norbornane (CHEBI:71546)"><img border="0" data-original-height="460" data-original-width="460" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHHEVJ1lLFisZzr6YFRwxyMvKKcCM5esragtINT0azeYznRUFg9V0pYYWxJFhVy9Bq3mTXn3BbhUIWipKAVsEtfC6TDPcc-ZGR6PqDeFhxNnftsrasNlhWfmBWF-XlXL4LU2T0jA/w200-h200/norbornane.jpg" width="200" /></a></td></tr>
<tr><th align="center">(b)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="2" type="a">
<li> norbornane (<i>trivial</i>) <br />
bicyclo[2.2.1]heptane (<a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog"><i>von Baeyer</i></a>) </li>
</ol>
</td>
</tr>
</table>
</center>
<a name='more'></a>
<p> You may recall that we <a href="http://metallome.blogspot.com/2021/01/chains-and-rings.html" target="_blank" title="Chains and rings @ this blog">defined</a> <i>trail</i> as a walk in which all edges are distinct, and <i>cycle</i> as a trail in which the only repeated vertices are the first and last vertices. Let’s number the carbon atoms in <b>(b)</b> like this: </p>
<center>
<table>
<tr>
<td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9769HgXoJURn5H2xcK81SZfycol3RX30XAu6ZdYYAIcATGPiGihWwsLKmB1ijNxQLEltiXKCAViTBmiaF_zQuXsrsf_9tfdUqD6DgACdglqy5YQ15w2VX4Q8oVVmJ022XujnVag/s460/norbornane.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="460" data-original-width="460" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9769HgXoJURn5H2xcK81SZfycol3RX30XAu6ZdYYAIcATGPiGihWwsLKmB1ijNxQLEltiXKCAViTBmiaF_zQuXsrsf_9tfdUqD6DgACdglqy5YQ15w2VX4Q8oVVmJ022XujnVag/w200-h200/norbornane.jpg" width="200" /></a></td></tr>
</table>
</center>
<p> So we can see that there are three different cycles in <b>(b)</b>: 1–2–3–4–5–6–1; 1–2–3–4–7–1; and 1–7–4–5–6–1.</p>
<p> On the other hand, chemists often look for the <i>minimum</i> number of cycles required to describe a ring system, which is equivalent to the minimum number of edges (i.e. bonds) we need to remove from the graph (structure) to turn it from cyclic to acyclic [<a href="#Zamora_1979" title="Zamora (1979)">1</a>—<a href="#García-Domenech_2008" title="García-Domenech (2008)">3</a>]. Think about it while you cut up the six-pack plastic rings. This number μ, variously known as <a href="http://en.wikipedia.org/wiki/Circuit_rank" target="_blank" title="Circuit rank in Wikipedia">circuit rank</a>, cyclomatic number, Frèrejacque number or nullity, is defined as </p>
<center><blockquote> μ = |<i>E</i>| − |<i>V</i>| + |<i>C</i>| </blockquote></center>
<p> where |<i>E</i>| is the number of edges (size), |<i>V</i>| is number of vertices (order) and |<i>C</i>| is the number of <a href="http://en.wikipedia.org/wiki/Component_(graph_theory)" target="_blank" title="Component (graph theory) in Wikipedia">connected components</a> of the graph. For one-component graph, |<i>C</i>| = 1. Thus, for <b>(a)</b> μ = 14 − 13 + 1 = 2 and for <b>(b)</b> μ = 8 − 7 + 1 = 2. In other words, both structures are bicyclic. </p>
<p> There are several possible scenarios for mutual arrangement of two cycles which result in very different names. </p>
<ol type="I">
<li> Two rings have no atoms in common and are linked to each other via at least one atom as in <b>(a)</b>. </li>
<li> Two rings have no atoms in common and are directly linked to each other via a single or double bond as in <b>(c)</b>. Such structures are known as <a href="http://metallome.blogspot.com/2021/07/ring-assemblies.html" target="_blank" title="Ring assemblies @ this blog"><i>ring assemblies</i></a>. If the ring components are identical, a variant of <a href="http://metallome.blogspot.com/2020/09/multiplicative-names.html" target="_blank" title="Multiplicative names @ this blog">multiplicative nomenclature</a> is used; otherwise, the structure is named <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">substitutively</a>. </li>
<li> Two rings have one atom in common as in <b>(d)</b>. Such arrangements are named according to <a href="http://metallome.blogspot.com/2021//06/spiro-names.html" target="_blank" title="Spiro names @ this blog">spiro nomenclature</a> [<a href="#Moss_1999a" title="Moss (1999a)">4</a>]. </li>
<li> Two mancude rings have two atoms in common as in <b>(e)</b>. Such systems are named using <a href="http://metallome.blogspot.com/2021/05/fused-ring-names.html" target="_blank" title="Fused ring names @ this blog">fused ring nomenclature</a> [<a href="#Moss_1998" title="Moss (1998)">5</a>]. </li>
<li> Two saturated rings have two or more atoms in common as in <b>(b)</b>. Such systems are named using <a href="http://metallome.blogspot.com/2021/05/von-baeyer-names.html" target="_blank" title="von Baeyer names @ this blog">von Baeyer nomenclature</a> [<a href="#Moss_1999b" title="Moss (1999b)">6</a>]. </li>
</ol>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30985" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="4,4'-bipyridine (CHEBI:30985)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiI-OBlhyGn3NGlBhkMNZVRo0FyqOrE7dJcBySeTOb5S5lYZNjxO7mfenbTTFVnqMgJI-5lsN9czTF0wwhL2KXe_WrLLunQ90goPo82h3p4e7K2SCnXVijB6mBGaYvCmQOPYo8-5A/w200-h200/4%252C4%2527-bipyridine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36754" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="vetispirane (CHEBI:36754)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcsf7uso2nYrM9Nn8hpkRQwGKS10Adh_HxA-TyUmky2uumbgWdGTKG-YxjY0g7Tc-bIZOGtl_DCHdp59gXZGsX0-sWmzDHpr213hG7THZwo7WCcM_C63u4C-GOFaScLr_ugExhCA/w200-h200/vetispirane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35858" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1-benzothiophene (CHEBI:35858)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijHAR5rNoMWsDehWA2mikVDIFvVWdR8W0UnBuIEd7nrll7irN60yBcFCkvlqyqNEwrHGL7J7zWACvyahyphenhyphenk8eOAAKPGOETRBXP9PwCwNuOZPRY_2cy5u6RZX7a8L5klh7AOlZAVlw/w200-h200/1-benzothiophene.png" width="200" /></a></td></tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th> <th align="center">(e)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> 4,4′-bipyridine (<i>ring assembly</i>) </li>
<li> vetispirane (<i>trivial</i>) <br />
6,10-dimethyl-2-(propan-2-yl)spiro[4.5]decane (<i>spiro + substitutive</i>) </li>
<li> 1-benzothiophene (<i>fused ring</i>) <br />
benzo[<i>b</i>]thiophene (<i>fused ring</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Edward W. Godly calls the scenarios II—V “rings in close association” [<a href="#Godly_1995" title="Godly (1995)">7</a>, p. 6] and the scenario I, surprise surprise, “rings not in close association” [<a href="#Godly_1995" title="Godly (1995)">7</a>, p. 55]. </p>
<h4> References </h4>
<ol>
<a name="Zamora_1979"></a>
<li> Zamora, A. (1979) An algorithm for finding the smallest set of smallest rings. <a href="http://doi.org/10.1021/ci60005a013" target="_blank" title="Zamora (1979) J. Chem. Inf. Comput. Sci. 16, 40-43."><i>Journal of Chemical Information and Computer Sciences</i> <b>16</b>, 40—43</a>. </li>
<a name="Downs_1989"></a>
<li> Downs, G.M., Gillet, V.J., Holliday, J.D. and Lynch, M.F. (1989) Review of ring perception algorithms for chemical graphs. <a href="http://doi.org/10.1021/ci00063a007" target="_blank" title="Downs et al. (1989) J. Chem. Inf. Comput. Sci. 29, 172-187."><i>Journal of Chemical Information and Computer Sciences</i> <b>29</b>, 172—187</a>. </li>
<a name="García-Domenech_2008"></a>
<li> García-Domenech, R., Gálvez, J., de Julián-Ortiz, J.V. and Pogliani, L. (2008) Some new trends in chemical graph theory. <a href="http://doi.org/10.1021/cr0780006" target="_blank" title="García-Domenech et al. (2008) Chem. Rev. 108, 1127-1169."><i>Chemical Reviews</i> <b>108</b>, 1127—1169</a>. </li>
<a name="Moss_1999a"></a>
<li> Moss, G.P. (1999) Extension and revision of the nomenclature for spiro compounds (IUPAC Recommendations 1999). <a href="http://doi.org/10.1351/pac199971030531" target="_blank" title="Moss (1999) Pure Appl. Chem. 71, 531-558."><i>Pure and Applied Chemistry</i> <b>71</b>, 531-558</a>. </li>
<a name="Moss_1998"></a>
<li> Moss, G.P. (1998) Nomenclature of fused and bridged fused ring systems (IUPAC Recommendations 1998). <a href="http://doi.org/10.1351/pac199870010143" target="_blank" title="Moss (1998) Pure Appl. Chem. 70, 143-216."><i>Pure and Applied Chemistry</i> <b>70</b>, 143—216</a>. </li>
<a name="Moss_1999b"></a>
<li> Moss, G.P. (1999) Extension and revision of the von Baeyer system for naming polycyclic compounds (including bicyclic compounds) (IUPAC Recommendations 1999). <a href="http://doi.org/10.1351/pac199971030513" target="_blank" title="Moss (1999) Pure Appl. Chem. 71, 513-529."><i>Pure and Applied Chemistry</i> <b>71</b>, 513—529</a>. </li>
<a name="Godly_1995"></a>
<li> Godly, E.W. <a href="https://amzn.to/3r2CR0E" target="_blank" title="Naming Organic Compounds: A Systematic Instruction Manual @ Amazon.co.uk"><i>Naming Organic Compounds: A Systematic Instruction Manual</i></a>, 2<sup>nd</sup> Ed. Ellis Horwood, Hemel Hempstead, 1995. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-13679116123244090042021-04-23T15:00:00.018+01:002023-08-07T10:00:30.569+01:00The many names of crowns<p> What is the best way to name the structure <b>(a)</b>? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32400" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="9-crown-3 (CHEBI:32400)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3zPnWaQ0f-3YaBiMDnHhfZlK5oB8rYyFRw77kXYs_6GlB7fimH3Z_zZT0oBIv1Q5AisvKvAJ1jnJxXz0_PQew6z7EYivUPh2dhuRLuK3kb9jzRTSPdC9QxsVgtSUwtOTlQ6gjlw/w200-h200/9-crown-3.png" width="200" /></a></td></tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="1" type="a">
<li> 1,4,7-trioxonane (<i>Hantzsch-Widman</i>) <br />
1,4,7-trioxacyclononane (<i>replacement</i>) <br />
cyclo[tri(oxyethylene)] (<i>organic macrocycle</i>) <br />
9-crown-3 (<i>Pedersen</i>) <br />
9<O<sub>3</sub>coronand-3> (<i>Vögtle-Weber</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The general naming method is <a href="http://metallome.blogspot.com/2020/06/skeletal-replacement-nomenclature.html" target="_blank" title="Skeletal replacement nomenclature @ this blog">skeletal replacement</a> applied to the corresponding carbocyclic parent hydride, in our case cyclononane, thus 1,4,7-trioxacyclononane. Or we can use extended <a href="http://metallome.blogspot.com/2021/04/hantzsch-widman-names.html" target="_blank" title="Hantzsch-Widman names @ this blog">Hantzsch-Widman</a> (H-W) system and call it 1,4,7-trioxonane. For rings with up to ten members, the H-W names are preferred [<a href="#Red_Book_2005" title="Red Book (2005)">1</a>, p. 96]. </p>
<p> What about the structures <b>(b)</b>—<b>(d)</b> then? Since all of these rings have more than ten members, we cannot use H-W system, so we have to give them replacement names: 1,4,7,10-tetraoxacyclododecane <b>(b)</b>, 1,4,7,10,13-pentaoxacyclopentadecane <b>(c)</b>, 1,4,7,10,13,16-hexaoxacyclooctadecane <b>(d)</b>. Rather long, completely unambiguous, and very boring.
<a name='more'></a>
The situation is akin to that with <a href="http://metallome.blogspot.com/2021/03/mancude-rings-and-annulenes.html" target="_blank" title="Mancude rings and annulenes @ this blog">annulenes</a>: as the rings grow in size, their systematic names also grow longer without reflecting the simple fact that all these structures consist of the same repeating unit. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32399" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="12-crown-4 (CHEBI:32399)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhK68sW-A6SMpoR8h-QyQMnW5gxuJKi1DEM5ErixEAxrg7qWrnGTU8aiFCmDCjsa9BDiYEDFpHGOIDtAbPcEF3DfpNcDQnGdu8EOnOZS1B4-Un0F3jjdmbQTspJkADdb0Z87sjMtg/w200-h200/12-crown-4.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32401" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="15-crown-5 (CHEBI:32401)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnIo7UHJuTCoMiMomjPqq0fxZ7z9KfdZWGkt8-0svHUxSOhp5ZmepJ1BQCfFmyxjmizOl8K5zEYNak1vqB8-t9S24-GFz2N_iqSy__uvwTYm8mKau7rb6fvDDKWvonMXID1w-iTg/w200-h200/15-crown-5.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32397" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="18-crown-6 (CHEBI:32397)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi85sKODeW6hE8vo-ZvGftvrykuPjgqKC680YfaqaJMFJ8N-XlLpYcBMIp0AfBbvrFp02YWPFyy7qc71fbM1abc_ptlUgQo9OVwvIFeG_AkUnhfP5ZDUQT_wsu-XmwD1r93rs_mRA/w200-h200/18-crown-6.png" width="200" /></a></td></tr>
<tr><th align="center">(b)</th> <th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="2" type="a">
<li> 1,4,7,10-tetraoxacyclododecane (<i>replacement</i>) <br />
cyclo[tetra(oxyethylene)] (<i>organic macrocycle</i>) <br />
12-crown-4 (<i>Pedersen</i>) <br />
12<O<sub>4</sub>coronand-4> (<i>Vögtle-Weber</i>) </li>
<li> 1,4,7,10,13-pentaoxacyclopentadecane (<i>replacement</i>) <br />
cyclo[penta(oxyethylene)] (<i>organic macrocycle</i>) <br />
15-crown-5 (<i>Pedersen</i>) <br />
15<O<sub>5</sub>coronand-5> (<i>Vögtle-Weber</i>) </li>
<li> 1,4,7,10,13,16-hexaoxacyclooctadecane (<i>replacement</i>) <br />
cyclo[hexa(oxyethylene)] (<i>organic macrocycle</i>) <br />
18-crown-6 (<i>Pedersen</i>) <br />
18<O<sub>6</sub>coronand-6> (<i>Vögtle-Weber</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The structures like <b>(a)</b>—<b>(d)</b> are known as <a href="http://en.wikipedia.org/wiki/Crown_ether" target="_blank" title="Crown ether in Wikipedia">crown ethers</a>. They could be defined as macrocycles consisting of several oxyethylene (–CH<sub>2</sub>–CH<sub>2</sub>–O–) groups. Adopting the IUPAC nomenclature for cyclic organic macromolecules [<a href="#Mormann_and_Hellwich_2008" title="Mormann & Hellwich (2008)">2</a>] which recommends names of the form ‘cyclo[poly(constitutional repeating unit)]’, we can assign the names cyclo[tri(oxyethylene)] to <b>(a)</b>, cyclo[tetra(oxyethylene)] to <b>(b)</b> and so on<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>. That’s better, isn’t it? No locants have to be cited, which is always a good news. </p>
<p> Another nomenclature system was proposed by the discoverer of crown ethers himself, <a href="http://en.wikipedia.org/wiki/Charles_J._Pedersen" target="_blank" title="Charles J. Pedersen in Wikipedia">Charles J. Pedersen</a> (1904—1989) in his seminal 1967 paper [<a href="#Pedersen_1967" title="Pedersen (1967)">3</a>]. He came up with short names of the form <i>m</i>-crown-<i>n</i>, where <i>m</i> is the ring size and <i>n</i> is the number of oxygen atoms in the ring. In some variants of Pedersen names, the first number is taken in square brackets, as in [18]crown-6 for <b>(d)</b>, perhaps by analogy with annulenes, perhaps to stress that this number is <i>not</i> a locant (in Pedersen system, no locants are needed for unsubstituted crowns). For any crown ether that is cyclo[<i>n</i>(oxyethylene)] it is easy to reconstruct the structure from the name like <i>m</i>-crown-<i>n</i>. Moreover, since <i>m</i> = 3<i>n</i>, one can argue that even this short name is redundant; e.g., for the structure <b>(d)</b> either 18-crown or crown-6 would suffice. I would go for the latter since the number of oxygen atoms is more important. </p>
<p> Problems arise when we try to use the simple system to name the molecules that deviate from cyclo[<i>n</i>(oxyethylene)] formula. Not satisfied with Pedersen names, Vögtle and Weber developed a more comprehensive nomenclature in an attempt to cover <a href="http://goldbook.iupac.org/terms/view/C01426" target="_blank" title="cryptand in Gold Book">cryptands</a> and podands in addition to <a href="http://goldbook.iupac.org/terms/view/C01421" target="_blank" title="crown in Gold Book">crowns</a> [<a href="#Weber_and_Vögtle_1980" title="Weber & Vögtle (1980)">4</a>, <a href="#Weber_and_Vögtle_1985" title="Weber & Vögtle (1985)">5</a>]. In their system, crowns are named ‘coronands’; for instance, the proposed name for <b>(d)</b> is 18<O<sub>6</sub>coronand-6><sup><a href="#Footnote_†" title="Footnote †">†</a></sup>. Further, <a href="http://en.wikipedia.org/wiki/Donald_J._Cram" target="_blank" title="Donald J. Cram in Wikipedia">Donald James Cram</a> (1919—2001), who would share the 1987 Nobel Prize in Chemistry with Pedersen and <a href="http://en.wikipedia.org/wiki/Jean-Marie_Lehn" target="_blank" title="Jean-Marie Lehn in Wikipedia">Jean-Marie Lehn</a>, suggested to shorten ‘coronands’ to ‘corands’ [<a href="#Cram_1986" title="Cram (1986)">6</a>]. Perhaps he was driven by desire to bring it in line with two-syllable ‘cryptands’, ‘podands’ and his own ‘spherands’, but, in doing so, he created a nonsensical term that is still longer than ‘crown’. </p>
<p> Now let’s have a look at the <a href="http://lothruput.blogspot.com/2021/04/this-is-extent-of-serendipity.html" target="_blank" title="this is the extent of serendipity @ low-throughput">first ever crown</a> discovered by Pedersen <b>(e)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:358732" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="dibenzo-18-crown-6 (CHEBI:358732)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhA086evBqxCf8hDIWHPUPIKn2RdgTDf9yTdGS1zoY2DxZkQBTIBEawNGCnSIYBWTiNjkGl1v54OS1Cc69N3GC7_qoaqdz-xRu3PfKgWpx1RvVGTNMxRyQO3ZWJltpV9IUmpbaA6Q/w200-h200/dibenzo-18-crown-6.png" width="200" /></a></td></tr>
<tr><th align="center">(e)</th>
</tr>
</table>
</center>
<center>
<table>
<tr><td><ol start="5" type="a">
<li> dibenzo[<i>b</i>,<i>k</i>][1,4,7,10,13,16]hexaoxacyclooctadecane (<i>replacement + <a href="http://metallome.blogspot.com/2021/05/fused-ring-names.html" target="_blank" title="Fused ring names @ this blog">fused ring</a></i>) <br />
dibenzo-18-crown-6 (<i>Pedersen</i>) <br />
18<O<sub>6</sub>(1,2)benzeno.2<sub>2</sub>.(1,2)benzeno.2<sub>2</sub>coronand-6> (<i>Vögtle-Weber</i>) <br />
2,5,8,10,13,16-hexaoxa-1,9(1,2)-dibenzenacyclohexadecaphane (<i><a href="http://www.qmul.ac.uk/sbcs/iupac/phane/" target="_blank" title="Phane Nomenclature, Part I: Phane Parent Names (IUPAC Recommendations 1998) @ IUPAC Chemical Nomenclature">phane</a> + replacement</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Pedersen named this molecule dibenzo-18-crown-6. Now there are three possible ways to fuse two benzene rings with 18-crown-6 <b>(d)</b> and so Pedersen name may appear ambiguous. Not that he wasn’t aware of that. He wrote [<a href="#Pedersen_1967" title="Pedersen (1967)">3</a>]: </p>
<blockquote> The placements of the hydrocarbon rings and the oxygen atoms are as symmetrical as possible in most cases, and the exceptions are indicated by <i>asym</i>. </blockquote>
<p> So there. Since there is no <i>asym</i> in the name, dibenzo-18-crown-6 must correspond to the most symmetrical isomer. Compare that with Vögtle-Weber’s 18<O<sub>6</sub>(1,2)benzeno.2<sub>2</sub>.(1,2)benzeno.2<sub>2</sub>coronand-6> which is not significantly shorter than “cumbersome and less illustrative” [<a href="#Weber_and_Vögtle_1985" title="Weber & Vögtle (1985)">5</a>, p. 3] IUPAC name, dibenzo[<i>b</i>,<i>k</i>][1,4,7,10,13,16]hexaoxacyclooctadecane, and you will understand why chemists still stick to Pedersen names in spite of all their limitations. </p>
<p> Crowns can contain heteroatoms other than oxygen: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37418" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,4,7-trithionane (CHEBI:37418)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgENvJ_fde5UeInU3V9ZTh4HMjPBxwZ0Egt75K6xCPDPRmNHrXAptHRPhsiNLF0bC_4A-oT8UrIFq-21SvXbdnHzTExvcwCeYV1c1uNDAHQ4fhi3bGyVotgOfMfOwGH5nSvQ_kzVg/w200-h200/1%252C4%252C7-trithionane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37391" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,4,7,10-tetraazacyclododecane (CHEBI:37391)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjk8z0CIJqaHZfsDhxpjpUOboFiXVoa8doqAK2M86GsXnJ90GqYpFp9shCluGdBdngv1pwf62UeDjrDtzzKVMPUCsbfctQ5EPo3YgKeZKeiISjYN3udvRZ-H_27sdFMkoeFHdyQhA/s1600/1%252C4%252C7%252C10-tetraazacyclododecane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37443" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,10-dioxa-4,7,13,16-tetraphosphacyclooctadecane (CHEBI:37443)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoj9RVraJm8UPwSPXDWn-Z544_jl_W-nHy3uixKWitW4w1WIfKJlkhCOmbYjGbkmqE9v8VpUrsfZBniKZU0IR_IPFGK5rmf397Svfgz2QiTTbo3fBjQtqI_HWSzJIdjB7kk6xayw/w200-h200/18aneP4O2.png" width="200" /></a></td></tr>
<tr><th align="center">(f)</th> <th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="6" type="a">
<li> 1,4,7-trithionane (<i>Hantzsch-Widman</i>) <br />
1,4,7-trithiacyclononane (<i>replacement</i>) <br />
cyclo[tri(sulfanediylethylene)] (<i>organic macrocycle</i>) <br />
trithia-9-crown-3 (<i>Pedersen + replacement</i>) <br />
[9]aneS<sub>3</sub> (<i>abbreviated ligand name</i>) <br />
9<S<sub>3</sub>coronand-3> (<i>Vögtle-Weber</i>) </li>
<li> cyclen (<i>trivial</i>) <br />
1,4,7,10-tetraazacyclododecane (<i>replacement</i>) <br />
tetraaza-12-crown-4 (<i>Pedersen + replacement</i>) <br />
cyclo[tetra(iminoethylene)] (<i>organic macrocycle</i>) <br />
[12]aneN<sub>4</sub> (<i>abbreviated ligand name</i>) <br />
12<N<sub>4</sub>coronand-4> (<i>Vögtle-Weber</i>) </li>
<li> 1,10-dioxa-4,7,13,16-tetraphosphacyclooctadecane (<i>replacement</i>) <br />
4,7,13,16-tetraphospha-18-crown-6 (<i>Pedersen + replacement</i>) <br />
[18]aneP<sub>4</sub>O<sub>2</sub> (<i>abbreviated ligand name</i>) <br />
18<OPPOPP-coronand-6> (<i>Vögtle-Weber</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Sulfur-containing crowns are variously referred to as ‘thiacrowns’, ‘crown thioethers’ [<a href="#Cooper_1988" title="Cooper (1988)">7</a>] or ‘coronand sulfides’ [<a href="#Weber_and_Vögtle_1985" title="Weber & Vögtle (1985)">5</a>, p. 7], and nitrogen-containing ones as ‘azacrowns’, ‘crown amines’, or ‘coronand amines’ [<a href="#Weber_and_Vögtle_1985" title="Weber & Vögtle (1985)">5</a>, p. 7]. For crowns with only one type of heteroatom, modified Pedersen names like trithia-9-crown-3 for <b>(f)</b> or tetraaza-12-crown-4 for <b>(g)</b> have been used in the literature although it would be more correct to call them trithio-9-crown-3 and tetraimino-12-crown-4, respectively<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>. We can also create “macrocyclic” names such as cyclo[tri(sulfanediylethylene)] for <b>(f)</b> and cyclo[tetra(iminoethylene)] for <b>(g)</b>. As soon another type of heteroatom makes its way into a crown, such relatively simple names are out of question. To avoid ambiguity, we’ve got to use locants, so I guess we’re better off with old H-W or replacement names. To quote Gokel & Fedders [<a href="#Gokel_and_Fedders_1996" title="Gokel & Fedders (1996)">8</a>], </p>
<blockquote> For the time being, the nomenclature of crowns and other heteromacrocycles will likely remain imperfect due to the inherent complexity of the structures. Nevertheless, standard heterocycle naming practices should be applied but often have not been. For example, crowns containing O, S, and/or N should be numbered starting with O rather than one of the atoms differentiating the compound from a simple crown. </blockquote>
<p> So we can name <b>(h)</b> 4,7,13,16-tetraphospha-18-crown-6, which is still shorter than 1,10-dioxa-4,7,13,16-tetraphosphacyclooctadecane. Another unambiguous alternative is a Vögtle-Weber-type name which I suppose is 18<OPPOPP-coronand-6> (where ‘OPPOPP’ is the sequence of heteroatoms), but don’t quote me on that. Meanwhile, IUPAC recommends abbreviated ligand names such as [9]aneS<sub>3</sub> <b>(f)</b>, [12]aneN<sub>4</sub> <b>(g)</b> and [18]aneP<sub>4</sub>O<sub>2</sub> <b>(h)</b> [<a href="#Red_Book_2005" title="Red Book (2005)">1</a>, Table VII, p. 261]. </p>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> The recommendations [<a href="#Mormann_and_Hellwich_2008">2</a>, p. 209] explicitly state: “The same format can be used for oligomer nomenclature, e.g., cyclo[tetra(constitutional repeating unit)].” So I am not making this up. </td>
</tr>
<tr><td valign="top">†</td>
<td> Specified by Weber and Vögtle thus [<a href="#Weber_and_Vögtle_1985" title="Weber & Vögtle (1985)">5</a>]:
<blockquote> The number preceding the angular brackets ‘< >’ indicates the ring size. In the presence of aromatic and heteroaromatic units in the ring, the shortest way to the next donor atom is considered. The angular brackets contain in the order given: 1) donor heteroatoms expressed by elemental symbols; 2) bridges, i.e. C–C chains between the donor atoms, denoted by numbers which correspond to the bridging C-atoms, bridge units like aromatic nuclei or more complex groups (position marked in round brackets). The designation ‘2’ for ethano, the most common bridge, is omitted if only this kind of bridge unit is present or if such a procedure does not curtail the clarity of the structure (cf. 18<O<sub>6</sub>coronand-6>); 3) the class name (e.g. coronand), and 4) the total number of donor heteroatoms. </blockquote> </td></tr>
<tr><td valign="top">‡</td>
<td> In general and organic chemical nomenclature, ‘<a href="http://goldbook.iupac.org/terms/view/T06347" target="_blank" title="thio in Gold Book">thio</a>’ means replacement of any <i>oxygen</i> atom with a sulfur atom. In organic nomenclature, ‘imino’ refers to replacement of an <i>endocyclic oxygen</i> atom by a nitrogen atom. On the other hand, in skeletal replacement nomenclature, ‘aza’ and ‘thia’ denote replacement of <i>carbon</i> with nitrogen and sulfur, respectively. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
<a name="Mormann_and_Hellwich_2008"></a>
<li> Mormann, W. and Hellwich, K.-H. (2008) Structure-based nomenclature for cyclic organic macromolecules (IUPAC Recommendations 2008). <a href="http://doi.org/10.1351/pac200880020201" target="_blank" title="Mormann & Hellwich (2008) Pure Appl. Chem. 80, 201-232."><i>Pure and Applied Chemistry</i> <b>80</b>, 201—232</a>. </li>
<a name="Pedersen_1967"></a>
<li> Pedersen, C.J. (1967) Cyclic polyethers and their complexes with metal salts. <a href="http://doi.org/10.1021/ja01002a035" target="_blank" title="Pedersen (1967) J. Am. Chem. Soc. 1967, 89, 7017-7036."><i>Journal of the American Chemical Society</i> <b>89</b>, 7017—7036</a>. </li>
<a name="Weber_and_Vögtle_1980"></a>
<li> Weber, E. and Vögtle, F. (1980) Classification and nomenclature of coronands, cryptands, podands, and of their complexes. <a href="http://doi.org/10.1016/S0020-1693(00)80096-1" target="_blank" title="Weber and Vögtle (1980) Inorg. Chim. Acta 45, L65-L67."><i>Inorganica Chimica Acta</i> <b>45</b>, L65—L67</a>. </li>
<a name="Weber_and_Vögtle_1985"></a>
<li> Weber, E. and Vögtle, F. <a href="http://doi.org/10.1007/978-3-642-70108-5_1" target="_blank" title="Weber and Vögtle (1985) Host Guest Complex Chemistry / Macrocycles, pp. 1-41.">Crown-type compounds — An introductory overview</a>. <i>In:</i> Vögtle, F. and Weber, E. (eds.) <a href="http://doi.org/10.1007/978-3-642-70108-5" target="_blank" title="Vögtle and Weber (Eds.) Host Guest Complex Chemistry / Macrocycles."><i>Host Guest Complex Chemistry / Macrocycles</i></a>. Springer-Verlag, Berlin, Heidelberg, 1985, pp. 1—41. </li>
<a name="Cram_1986"></a>
<li> Cram, D.J. (1986) Preorganization — From solvents to spherands. <a href="http://doi.org/10.1002/anie.198610393" target="_blank" title="Cram (1986) Angew. Chem. Int. Ed. Engl. 25, 1039-1057."><i>Angewandte Chemie International Edition in English</i> <b>25</b>, 1039—1057</a>. </li>
<a name="Cooper_1988"></a>
<li> Cooper, C.R. (1988) Crown thioether chemistry. <a href="http://doi.org/10.1021/ar00148a002" target="_blank" title="Cooper (1988) Acc. Chem. Res. 21, 141–146."><i>Accounts of Chemical Research</i> <b>21</b>, 141—146</a>.</li>
<a name="Gokel_and_Fedders_1996"></a>
<li> Gokel, G.W. and Fedders, M.F. (1996) Ten-membered rings or larger with one or more nitrogen and oxygen and/or sulfur atoms. <a href="http://doi.org/10.1016/B978-008096518-5.00239-2" target="_blank" title="Gokel & Fedders (1996) Comprehensive Heterocyclic Chemistry II 9, 863-892."><i>Comprehensive Heterocyclic Chemistry II</i> vol. <b>9</b>, 863—892</a>.</li> </ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-51515500528809081752021-04-05T23:00:00.046+01:002024-03-17T00:24:21.533+00:00Hantzsch-Widman names<p> Are you tired of carbocycles? Let’s have some ring diversity, I say. </p>
<p> Structures that contain two or more different elements in a ring are called <a href="http://goldbook.iupac.org/terms/view/H02798" target="_blank" title="heterocyclic compounds in Gold Book"><i>heterocyclic</i></a>. Perhaps because “<a href="http://en.wikipedia.org/wiki/Heteroatom" target="_blank" title="Heteroatom in Wikipedia">heteroatom</a>” is really an organic chemistry concept, the word “heterocycle” is commonly (mis)understood as “organic heterocycle”, that is, a carbocycle where at least one carbon atom is replaced by an heteroatom. I blame organic chemists for that. </p>
<p> For a small number of <a href="http://metallome.blogspot.com/p/monoheterocyclic-parent-hydrides.html" target="_blank" title="Monoheterocyclic parent hydrides @ this blog">five- and six-membered organic heterocycles</a> the trival names are retained to be used as parent hydride names. Note that, although “<a href="http://en.wikipedia.org/wiki/Trivial_name" target="_blank" title="Trivial name in Wikipedia">trivial</a>” in chemical parlance means “non-systematic”, there <i>is</i> a system to most of those names. For instance, we can see that imidazolidine <b>(a)</b> is a fully saturated version of 1<i>H</i>-imidazole <b>(b)</b>: </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33137" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="imidazolidine (CHEBI:33137)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjP-AqrybTnziUibAFW1uSZ9-5IZDQy7bQSKvjIZNexgK7CVVT2VKJcafFjuvMuQGKbpP2T866PB7-vDzWSrZPIUeW2iq-y8lE1l9FQHPm_quHJzuFcMHZsX9-FXPqWu-oLbn-SUw/w200-h200/imidazolidine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16069" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1H-imidazole (CHEBI:16069)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgdqTPi4upf5C7mvcOIbjxSnopzyFDwN2HUMrhGgN41xQ61AZqIX1agkZMwiYiSD__6a1UvVxQmzNJsEDbdOBkY38T6yUnRjJ4G8jUeNNBcqw9ETUrKAMTJr-Z9gx0qWYpRfZbFsw/w200-h200/1H-imidazole.png" width="200" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> imidazolidine </li>
<li> 1<i>H</i>-imidazole </li>
</ol>
</td>
</tr>
</table>
</center>
<a name='more'></a>
<p> Similar relationships can be observed between pyrrolidine and pyrrole, pyrazolidine and pyrazole. On the other hand, thiomorpholine <b>(c)</b> is morpholine <b>(d)</b> where an oxygen atom has been replaced by a sulfur atom, in accordance with the standard use of ‘<a href="http://goldbook.iupac.org/terms/view/T06347" target="_blank" title="thio in Gold Book">thio</a>’ in chemical nomenclature. Selenophene and tellurophene, predictably enough, are selenium and tellurium analogues of thiophene. So, some of these “trivial” names are in fact “semi-systematic” (or “semi-trivial”, whatever you prefer). Still, that’s about as far as you can get. There is a whole wide world of heterocycles and we need to be able to name them. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36392" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="thiomorpholine (CHEBI:36392)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg24OuTVAMXpiQTgwgHRUONeXXmVWY4kCm999wdtzwPUIYwUiwabRbn25XZzkYZtUnmVSPPixwPVkSnjiFzR8IX99V9DNzurda36pNoD7h5jlF2iBShJTapYmZ4QqhMEOfYh42bSA/w200-h200/thiomorpholine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:34856" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="morpholine (CHEBI:34856)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmDJlUz_UnMlPtNLXUIEZg8dL1YduWVtQ1z5QeSIYfpSjbQl3BBYkqlimtVKxASpUX1xoUrNtavYEXEyJIKGFmDYxd-L3D6TUOGfeMpjfYwff3Io9I76Lzmvjn5Et5GX5lwVKIOw/w200-h200/morpholine.png" width="200" /></a></td>
</tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> thiomorpholine </li>
<li> morpholine </li>
</ol>
</td>
</tr>
</table>
</center>
<p> There are two main methods of naming heterocycles systematically. One is to use <a href="http://metallome.blogspot.com/2020/06/skeletal-replacement-nomenclature.html" target="_blank" title="Skeletal replacement nomenclature @ this blog">skeletal replacement</a> nomenclature that we are already familiar with. Another one is the extended Hantzsch-Widman system [<a href="#Powell_1983" title="Powell (1983)">1</a>]. </p>
<p> This system is used to name saturated and <a href="http://metallome.blogspot.com/2021/03/mancude-rings-and-annulenes.html" target="_blank" title="Mancude rings and annulenes @ this blog">mancude</a> monocycles up to ten ring members. It is named after <a href="http://en.wikipedia.org/wiki/Arthur_Rudolf_Hantzsch" target="_blank" title="Arthur Rudolf Hantzsch in Wikipedia">Arthur Rudolf Hantzsch</a> and <a href="http://de.wikipedia.org/wiki/Oskar_Widman" target="_blank" title="Oskar Widman in German Wikipedia">Oskar Widman</a>, who independently introduced methods for naming five- and six-membered nitrogen-containing monocycles [<a href="#Hantzsch_Weber_1887" title="Hantzsch & Weber (1887)">2</a>, <a href="#Widman_1888" title="Widman (1888)">3</a>]. It would be more fair to call it Hantzsch-Weber-Widman system, but life is not fair and sadly the name of Hantzsch’s coauthor was all but forgotten — to the degree I can’t find any information on him, including his first names. On the other hand, this nomenclature system is sometimes referred to as <a href="http://de.wikipedia.org/wiki/Hantzsch-Widman-System" target="_blank" title="Hantzsch-Widman-System in German Wikipedia">Hantzsch-Widman-Patterson system</a>, in honour of Austin McDowell Patterson (1876—1956). </p>
<p> A Hantzsch-Widman (H-W) name minimally consists of at least one ‘a’ “prefix” followed by a “stem” [<a href="#Powell_1983" title="Powell (1983)">1</a>] or “ending” [<a href="#Red_Book_2005" title="Red Book (2005)">4</a>, p. 96] that indicate the size and saturation of the ring. We know by now that none of these word parts qualifies to be either prefix or ending because of their high semantic load. As <a href="http://metallome.blogspot.com/2020/10/prefixes-or-combining-forms.html" target="_blank" title="Prefixes — or combining forms? @ this blog">mentioned earlier</a>, skeletal replacement “prefixes” such as ‘aza’, ‘bora’, or ‘phospha’ are combining forms composed of roots ‘az’, ‘bor’, ‘phosph’, respectively, plus the functional morpheme ‘a’. The H-W “stems” are also combining forms composed of roots ‘epin’, ‘iren’, ‘olan’ etc. followed by ending ‘e’ which, in any case, is optional [<a href="#Powell_1983" title="Powell (1983)">1</a>, p. 413, note b]. Additionally, H-W names may contain <a href="http://metallome.blogspot.com/2020/10/prefixes-or-combining-forms.html" target="_blank" title="Prefixes — or combining forms? @ this blog">multipliers</a> (‘di’, ‘tri’, etc.) and locants. The H-W ring roots are summarised in the table below.
</p><div><br /></div>
<center>
<table width="70%">
<tr><th align="left">Order</th> <th align="left">Last-cited heteroatom</th> <th align="left">Mancude</th> <th align="left">Saturated</th> </tr>
<tr><th><p></p></th></tr>
<tr><th>3</th> <td></td> <td>irene / irine<sup>*</sup></td> <td>irane / iridine<sup>†</sup> </td> </tr>
<tr><th>4</th> <td></td> <td>ete</td> <td>etane / etidine<sup>†</sup> </td> </tr>
<tr><th>5</th> <td></td> <td>ole</td> <td>olane / olidine<sup>†</sup> </td> </tr>
<tr><th>6(A)</th> <td>O, S, Se, Te, Po, Bi</td> <td>ine</td> <td>ane</td> </tr>
<tr><th>6(B)</th> <td>N, Si, Ge, Sn, Pb</td> <td>ine</td> <td>inane</td> </tr>
<tr><th>6(C)</th> <td>F, Cl, Br, I, P, As, Sb, B, Al, Ga, In, Tl</td> <td>inine</td> <td>inane</td> </tr>
<tr><th>7</th> <td></td> <td>epine</td> <td>epane</td> </tr>
<tr><th>8</th> <td></td> <td>ocine</td> <td>ocane</td> </tr>
<tr><th>9</th> <td></td> <td>onine</td> <td>onane</td> </tr>
<tr><th>10</th> <td></td> <td>ecine</td> <td>ecane</td> </tr>
<tr><th><p></p></th></tr>
<tr><td></td> <td colspan="3">* For rings with nitrogen as only heteroatom</td></tr>
<tr><td></td> <td colspan="3">† For rings containing nitrogen</td></tr>
</table></center>
<p> You may remember that the substitutive names of carbocycles, except for benzene and benzene ring-containing structures, are based on the names of <a href="http://metallome.blogspot.com/2021/03/alicyclic-monocycles.html" target="_blank" title="Alicyclic monocycles @ this blog">cycloalkanes</a>, i.e. saturated parents. In the H-W system we have a choice. To name a saturated ring, we choose saturated root; to name an unsaturated ring, we pick mancude root. It’s best to see how it works looking at the examples: </p>
<center>
<table width="70%">
<tr><th>Order</th> <th>Saturation</th> <th align="center">Structure</th> <th align="center">Hantzsch-Widman name</th> <th align="left">Skeletal replacement name</th> </tr>
<tr><th><p></p></th></tr>
<tr><th>3</th> <td>saturated</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30977" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="thiirane (CHEBI:30977)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi81pHodqKtr6Xd9XBH_cWtwlzKGjPuARjoxvtDZwjf0oEaCYx6cAjU6QH53AbGsWGB6XglZ49pFWJ1W-Vtzgs3MsKohR0McpafX320RHu7kdRjDhIP1gkflcit4Ad11BmEx58RWw/w200-h200/thiirane.png" width="100" /></a> </td><td>thiirane</td> <td>thiacyclopropane</td> </tr>
<tr><th>3</th> <td>mancude</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30978" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="oxazirene (CHEBI:30978)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBKrY94c6IZ1-TiA25I50Wnshn8a6DHFsGzXzOvTZKDuan_7kljjyXt-3-pB9wYRJV0nB5GbiUDtIzrRMOr764cQRWE-RItQ2UWCcKVTIh5hffmoetjM9giufhkd8Z3m2DfoopiQ/w200-h200/oxazirene.png" width="100" /></a> </td><td>oxazirene</td> <td>1-oxa-2-azacycloprop-2-ene</td> </tr>
<tr><th>4</th> <td>saturated</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30968" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="azetidine (CHEBI:30968)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxp-ioNjpPxt4fHKr2x_sF5cGTIebZaZTWTKlnKT78kNyT866eCQsIPmqDBGcBHaNGCrbpJXXEO26p26YlbVN6GAqdyHCuR1HTYy83GYl42_GGtn4SU4bpNhauzwJDaiCF_IslZQ/w200-h200/azetidine.png" width="100" /></a> </td><td>azetidine</td> <td>azacyclobutane</td> </tr>
<tr><th>4</th> <td>mancude</td> <td><a href="https://www.chemspider.com/Chemical-Structure.57466098.html" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3-Disilete (ChemSpider 57466098)"><img border="0" data-original-height="250" data-original-width="250" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhMIZU6oweImcxjWNBOwYUEXE7Fk_JEmo_123eODMD2WP-RzUBuDzk0VY0WGuTMb3aP4xux3c0NjdlCqQxh_Qsr69trzm2L11S4T77SmAc3c5br0C7sOF60t5HOYGjo1aEDFm6Few/w200-h200/1%252C3-disilete.png" width="100" /></a></td> <td>1,3-disilete</td> <td>1,3-disilacyclobuta-1,3-diene</td> </tr>
<tr><th>5</th> <td>saturated</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:38079" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3-dithiolane (CHEBI:38079)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgs1nJ5H_oSKxfYsCNomJsHCqmH1u8Ae-YpiOI0H8EhY4sql4QJ_Jy2CEfPOsvW9gIfD2VN0gh271W1foaukS8Zrau9HJiwuYf3_fZHGUbRlo1mnDxNQ_2CnbKroCkx_dW0i2dFcg/w200-h200/1%252C3-dithiolane.png" width="100" /></a> </td><td>1,3-dithiolane</td> <td>1,3-dithiacyclopentane</td> </tr>
<tr><th>5</th> <td>mancude</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33131" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1H-arsole (CHEBI:33131)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrvKDZeGWTnRP9WLrkfB5cOawrldcY8I5q5-506XGZfey5zMejwTBK1IWxPn10Sb9Vyk5RIhPCCdloPupO2LaKcunU1gg277S3Q0wWbdFQfifyoW8_pgLSrahtxWv6W5f6S5pimg/w200-h200/1H-arsole.png" width="100" /></a> </td><td>1<i>H</i>-arsole</td> <td>arsacyclopenta-2,4-diene</td> </tr>
<tr><th>6</th> <td>saturated</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:38043" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3,5-trioxane (CHEBI:38043)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEilulRFIpmK5QxteMAUoKh2LCaVdd9fkGFnLfkls2D7dQrnQUFfZbtdbHLkY8wh4AekHukBvy6tNWNnn9L6oQNAlFNvIKKUTDs12ltjJeDtNcaJnMzki9qp8s5IEDbnqmMn8_xkEA/w200-h200/1%252C3%252C5-trioxane.png" width="100" /></a></td> <td>1,3,5-trioxane</td> <td>1,3,5-trioxacyclohexane</td> </tr>
<tr><th>6</th> <td>mancude</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30259" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3,5-triazine (CHEBI:30259)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-ZeFOJti4L4rvjCLWNV0yWoiMOYAWSLa6mV_91eyqlS1b547zlw4xhaJtW1dJgdzOk3gfzQXBNOo5LMSCko2nakwErT_lzNlpliUyLcv_M0lQboDhtvwX_3Kqafu-SGGNu8Uddg/w200-h200/1%252C3%252C5-triazine.png" width="100" /></a> </td><td>1,3,5-triazine</td> <td>1,3,5-triazabenzne</td> </tr>
<tr><th>7</th> <td>saturated</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:49106" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="oxepane (CHEBI:49106)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtj603C5e2eGk4YVfXYXL6Kk9iN41_NZjUQ6sJjhVfe367cprIJtnmfmb2Y2eCoaYApgJ8tqn8W4OEpQbWfDi0fnc-lchZ7yRkcskI8witgLAAztEm9dicxJd8Kgywb04alLZ2Pw/w200-h200/oxepane.png" width="100" /></a></td> <td>oxepane</td> <td>oxacycloheptane</td> </tr>
<tr><th>8</th> <td>saturated</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:142569" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,5-oxathiocane (CHEBI:142569)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgymFZICqhpyj-PiV4UpAjC3mUxG-6XLLsWPJl19nBCU84Kh4GTYOsAt_h_Cc1tFcO1T3wfUXXDhYkhV4Q7Mjbw-8QZysReAUhhJ8u3O4u7T6znYor_AYt5kQp-tH3cBTfc7p3KPg/w200-h200/1%252C5-oxathiocane.png" width="100" /></a></td> <td>1,5-oxathiocane </td> <td>1-oxa-5-thiacyclooctane</td> </tr>
<tr><th>9</th> <td>saturated</td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37405" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,4,7-triazonane (CHEBI:37405)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjb2FbI4-JaZmWOX4LiCCSaAH3qNElzPxbfvt7vMl6ACAM_tvJjCPpnDAL51hGln5bURvAwuhW8Kw7peXg0vrNgZgoJT-5eWL29f7spqm8LcINkM_gKoQ-5lwRsbAvIlvgJM7tthQ/w200-h200/1%252C4%252C7-triazonane.png" width="100" /></a></td> <td>1,4,7-triazonane</td> <td>1,4,7-triazacyclononane</td> </tr>
<tr><th>10</th> <td>saturated</td> <td><a href="https://www.chemspider.com/Chemical-Structure.121225.html" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3,5,7,9-Pentathiecane (ChemSpider 121225)"><img border="0" data-original-height="500" data-original-width="500" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgH3qn4f6X_M9z0kP9grBsyFCJpFbaJyRJ3Cxdc2WZtxmxkIViGw4usfsTNGFYKTO-TspFrpHMZslzi2aoZq47TWbWAyHJLpAXrV7wQbfNekPzSLd7uYO-1sKIzB4NwhKAq8VB37Q/w200-h200/1%252C3%252C5%252C7%252C9-pentathiecane.png" width="100" /></a></td> <td>1,3,5,7,9-pentathiecane</td> <td>1,3,5,7,9-pentathiacyclodecane</td> </tr>
</table></center>
<p> As you can see from these examples, H-W names are significantly shorter tham the corresponding replacement names. </p>
<p> A few observations. </p>
<p> Upon combining with a corresponding H-W root, a replacement (‘a’) term loses its characteristic final ‘a’ “when followed by a vowel” [<a href="#Powell_1983" title="Powell (1983)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/hetero/HW2t5.html#RB12" target="_blank" title="Revision of the extended Hantzsch-Widman system of nomenclature for heteromonocycles (Recommendations 1982). RB-1.2: Monocycle with up to ten ring members, one of which is a heteroatom">Rule RB-1.2</a>]<sup><a href="#Footnote_‡" title="Footnote ‡">‡</a></sup>. Since <i>all</i> H-W roots begin with a vowel, <i>all</i> replacement terms immediately preceding a H-W root lose the final ‘a’: <span style="background-color: paleturquoise;">az</span><span style="background-color: yellow;">etidine</span> (not <strike><span style="background-color: paleturquoise;">aza</span><span style="background-color: yellow;">etidine</span></strike>), 1,3-<span style="background-color: paleturquoise;">dithi</span><span style="background-color: yellow;">olane</span> (not 1,3-<strike><span style="background-color: paleturquoise;">dithia</span><span style="background-color: yellow;">olane</span></strike>), 1,3,5-<span style="background-color: paleturquoise;">triox</span><span style="background-color: yellow;">ane</span> (not 1,3,5-<strike><span style="background-color: paleturquoise;">trioxa</span><span style="background-color: yellow;">ane</span></strike>) and so on. This also happens if a replacement form is followed by <i>another</i> replacement term that begins with a vowel, as in <span style="background-color: paleturquoise;">oxaz</span><span style="background-color: yellow;">irene</span> (not <strike><span style="background-color: paleturquoise;">oxaaza</span><span style="background-color: yellow;">irene</span></strike>). By comparison, in skeletal replacement nomenclature the final ‘a’ of the replacement term is never omitted, whether the structure is acyclic or cyclic, as in 3,6,9,12,15,18-<span style="background-color: paleturquoise;">hexaoxa</span><span style="background-color: yellow;">icosane</span> or 1-<span style="background-color: paleturquoise;">oxa</span>-2-<span style="background-color: paleturquoise;">aza</span><span style="background-color: yellow;">cycloprop</span>-2-<span style="background-color: yellow;">ene</span>. </p>
<a name="Element_priority_sequence"></a>
<p> A heteromonocycle with two or more different heteroatoms is named according to the priority sequence <b>(1)</b>: </p>
<center><table><tr><td><blockquote> F > Cl > Br > I > O > S > Se > Te > N > P > As > Sb > Bi > Si > Ge > Sn > Pb > B > Al > Ga > In > Tl </blockquote></td><th>(1)</th></tr></table></center>
<p> thus <span style="background-color: paleturquoise;">oxaz</span><span style="background-color: yellow;">irene</span> (not <strike><span style="background-color: paleturquoise;">azox</span><span style="background-color: yellow;">irene</span></strike>), <span style="background-color: paleturquoise;">thiadiaz</span><span style="background-color: yellow;">ole</span> (not <strike><span style="background-color: paleturquoise;">diazathi</span><span style="background-color: yellow;">ole</span></strike>), etc. </p>
<p> Some mancude rings contain saturated atoms. To avoid ambiguity in the names, such atoms are specified using the <a href="http://goldbook.iupac.org/terms/view/I03004" target="_blank" title="indicated hydrogen in Gold Book">indicated hydrogen</a> descriptor, which consists of the locant followed by a hydrogen symbol, as in 1<i>H</i>-imidazole <b>(b)</b> (to distinguish it from <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51802" target="_blank" title="4H-imidazole (CHEBI:51802)">4<i>H</i>-imidazole</a>) or in <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33131" target="_blank" title="1H-arsole (CHEBI:33131)">1<i>H</i>-arsole</a> (because <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37178" target="_blank" title="2H-arsole (CHEBI:37178)">2<i>H</i></a>- and <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37179" target="_blank" title="3H-arsole (CHEBI:37179)">3<i>H</i></a>-tautomers are also possible). Unfortunately, indicated hydrogen, like most chemical descriptors, compromises pronounceability of resulting names.</p>
<p> What about unsaturated rings that are <i>not</i> mancude? In this case, one has to either start with mancude parent name and modify it <a href="http://metallome.blogspot.com/2020/09/additive-again.html" target="_blank" title="Additive again @ this blog">additively</a> with ‘dihydro’, ‘tetrahydro’, etc., or start with saturated parent name and modify it <a href="http://metallome.blogspot.com/2020/07/subtractive-names.html" target="_blank" title="Subtractive names @ this blog">subtractively</a> with ‘didehydro’, ‘tetradehydro’, etc. The first method is “usually preferred” [<a href="#Powell_1983" title="Powell (1983)">1</a>, <a href="http://www.qmul.ac.uk/sbcs/iupac/hetero/HW2t5.html#RB15" target="_blank" title="Revision of the extended Hantzsch-Widman system of nomenclature for heteromonocycles (Recommendations 1982). RB-1.5: Heteromonocycle with less than the maximum number of noncumulative double bonds">Rule RB-1.5</a>], although I personally would go for a method that results in a simpler name, avoiding, if possible, indicated hydrogen. For example, the structure <b>(e)</b> could be named either 2,3-<span style="background-color: lightgreen;">dihydro</span>-1<i>H</i>-1,2,4-<span style="background-color: paleturquoise;">triaz</span><span style="background-color: yellow;">ole</span> (additively) or 3,4-<span style="background-color: wheat;">didehydro</span>-1,2,4-<span style="background-color: paleturquoise;">triaz</span><span style="background-color: yellow;">olidine</span> (subtractively).
</p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51259" target="_blank" title="1,2,4-triazoline (CHEBI:51259)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFvRACYhWDy8ZEVyXFv_TgC52SVLu1nvKxeJIEenh7Mw_FF-niDH8kyas1XShkVzCBwGjntIWV1ihT9dXKlYScrhsyGDtbetGLpPTIuMQ4bajLde6oAZ-kW9TUMLY6Nd67mP7qpw/w200-h200/1%252C2%252C4-triazoline.png" width="200" /></a></td>
</tr>
<tr><th align="center">(e)</th></tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> 1,2,3-triazoline (<i>historic H-W, no longer recommended</i>) <br />
2,3-dihydro-1<i>H</i>-1,2,4-triazole (<i>H-W + additive</i>) <br />
3,4-didehydro-1,2,4-triazolidine (<i>H-W + subtractive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Although the H-W system was developed for organic heterocycles, i.e. default atom to be replaced is carbon, the ring to be named does not <i>need</i> to contain any carbon: </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33122" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclodiborathiane (CHEBI:33122)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTZ-07l_GT4lbWopB9FjGYHuz7VvjEreLQkDL1LSVvfTvOw2bMIlkDToa42K-LBvgNeKpsH6bfB15DkUHv7_Pm_FBUr63HtaFwpoAOfayFESqzYrG_KQG5sDCaOJ-WJUs3_iIqHg/w200-h200/cyclodiborathiane.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33119" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="borazine (CHEBI:33119)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFyRB4IcG_HM7bMi9gDtKpnBYJb0-GfKPvJnkoO-4sC-DFUkuWH9FO3SrSt9RUQHXTiahouzpR448iZjfH_Bp5ABrdcqJAVMcppihJZf9Hd05IFA88-BtZ0wLq-Kvnu-IjX2g3SA/w200-h200/borazine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:48145" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclotetrasiloxane (CHEBI:48145)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDZXOr8SoYfJhthsdyMpLo40Q_xYeI7gndiYhBQ8xgLn5Pra16Z_bTFKuCJigv-_Ihyphenhyphent2oRrSev7qLQ6NPWiDbP9mQn5yPI9qYp2LmVcGd_ncFALfate-famjNwQbGN5k0OEVnTg/w200-h200/cyclotetrasiloxane.png" width="200" /></a></td>
</tr>
<tr><th align="center">(f)</th> <th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="6" type="a">
<li> 1,3,2,4-dithiadiboretane (<i>H-W</i>) <br />
cyclodiborathiane (<i>NASA</i>) </li>
<li> borazine (<i>trivial</i>) <br />
1,3,5,2,4,6-triazatriborinane (<i>H-W</i>) <br />
1,3,5-triaza-2,4,6-triboracyclohexane (<i>replacement</i>) <br />
cyclotriborazane (<i>NASA</i>) </li>
<li>1,3,5,7,2,4,6,8-tetroxatetrasilocane (<i>H-W</i>) <br />
cyclotetrasiloxane (<i>NASA</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> I have to say that H-W names for the structures <b>(f)</b> — <b>(h)</b> somehow don’t appeal to me. They just have too many locants for my taste. Thankfully, there is yet <i>another</i> naming method “for the special case of saturated rings of two alternating skeletal atoms” [<a href="#Red_Book_2005" title="Red Book (2005)">4</a>, p. 96]. Here, the name for a cycle that contains <i>n</i> pairs of skeletal atoms –X–Y– consists of ‘cyclo’, followed by a multiplier for <i>n</i>, followed by the replacement terms for X and Y, followed by ‘ane’. For reasons unknown, here the replacement terms are cited in the <i>reverse</i> of the order of the priority sequence <b>(<a href="#Element_priority_sequence" title="Priority sequence (1)">1</a>)</b>. For want of a better name, I call this latter method NASA (for “<b><i>n</i></b> <b>a</b>lternating <b>s</b>keletal <b>a</b>toms”). One does not have to be an expert to see that cyclotetrasiloxane (note Si > O!) is a much more elegant name for <b>(h)</b> than 1,3,5,7,2,4,6,8-tetroxatetrasilocane (here O > Si). </p>
<p> Still, the extended H-W system could be used to name some inorganic heterocycles or, indeed, inorganic <a href="http://goldbook.iupac.org/terms/view/H02843" target="_blank" title="homocyclic compounds in Gold Book"><i>homocycles</i></a>: </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33123" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclotetraborane (CHEBI:33123)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSEjJWtfM1AFAl52VmCJrXrC9TDJyW4iomBvgwd6YkqfwVaXUmFstUrsVTjPSIZfAzyEtxUa0DzLYH4w5Zz2dOTFGxv1vUiXsyOKYPtQqQ_LhjFmgnL-RF2AGG-ZdhlvdnOLYEqg/s0/cyclotetraborane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36869" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="hexazine (CHEBI:36869)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgZIHWmH7HSOjGgtwiFuVE5uSZv0Da22kvehfr_Up51Xx2swBXQR7e-EZHdAII-7lRfvkaIOGDzJr0TiFi6g2wbrvIw7eaAglTYIaO5p38rnJkvO0hejgKFgaz9cgDVYg_FqrJ9xw/w200-h200/hexazine.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36912" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclooctaselenium (CHEBI:36912)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgI58Qz6AAafAa_IxJjv3J5xxhm6soxTyITRUWjjkqGs25qT4fHa6uN65epIdIGu52iA67bW46IUKke4WhdlNQXsEj9WFIxjsC-Oow7QPyLQ-pMeBiA8iCoumZAcQ1QhVQzZPMmOw/w200-h200/cyclooctaselenium.png" width="200" /></a></td>
</tr>
<tr><th align="center">(i)</th> <th align="center">(j)</th> <th align="center">(k)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="9" type="a">
<li> tetraboretane (<i>H-W</i>) <br />
cyclotetraborane(4) (<i>boron hydride nomenclature</i>) </li>
<li> hexazine (<i>H-W</i>) <br />
hexaazacyclohexa-1,3,5-triene (<i>replacement</i>) </li>
<li> <i>cyclo</i>-octaselenium <br />
octaselenocane (<i>H-W</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The only kind of cycles that are <i>not</i> named with H-W system are carbocycles, although I don’t see why one cannot do that. For once, the name ‘ocine’ is much shorter than ‘cycloocta-1,3,5,7-tetraene’ and even ‘[8]annulene’. </p>
<p> To sum up: </p>
<ul>
<li> The extended Hantzsch-Widman system can be used to name organic heterocycles, inorganic heterocycles, and inorganic homocycles up to ten members, with any number of heteroatoms from the list <b>(<a href="#Element_priority_sequence" title="Priority sequence (1)">1</a>)</b>; </li>
<li> A H-W name consists of two parts: replacement (‘a’) term(s) followed by a H-W ring root; </li>
<li> In the special case of saturated rings of two alternating skeletal atoms, another naming method (which I call NASA) can be employed; </li>
<li> For ring sizes greater than ten we have no choice but use skeletal replacement nomenclature. </li>
</ul>
<a name="Footnote_‡"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">‡</td>
<td> In a number of nomenclature publications, including [<a href="#Powell_1983" title="Powell (1983)">1</a>] and [<a href="#Red_Book_2005" title="Red Book (2005)">4</a>], this vowel loss is referred to as “<a href="http://en.wikipedia.org/wiki/Elision" target="_blank" title="Elision in Wikipedia">elision</a>”. I need to do more research on the topic because I am not convinced that this linguistic term is being used correctly. Watch this space. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<a name="Powell_1983"></a>
<li> Powell, W.H. (1983) Revision of the extended Hantzsch-Widman system of nomenclature for heteromonocycles.
<a href="http://doi.org/10.1351/pac198855020409" target="_blank" title="Powell (1983) Pure Appl. Chem. 55, 409-416."><i>Pure and Applied Chemistry</i> <b>55</b>, 409—416</a>. </li>
<a name="Hantzsch_Weber_1887"></a>
<li> Hantzsch, A. and Weber, J.H. (1887) Ueber Verbindungen des Thiazols (Pyridins der Thiophenreihe). <a href="http://zenodo.org/record/1425487" target="_blank" title="Hantzsch & Weber (1887) Ber. Dtsch. Chem. Ges. 20, 3118—3232."><i>Berichte der Deutschen Chemischen Gesellschaft</i> <b>20</b>, 3118–3232</a>. </li>
<a name="Widman_1888"></a>
<li> Widman, O. (1888) Zur Nomenclatur der Verbindungen, welche Stickstoffkerne enthalten. <a href="http://zenodo.org/record/1427940" target="_blank" title="Widman, O. (1888) J. Prakt. Chem. 38, 185-201."><i>Journal für praktische Chemie</i> <b>38</b>, 185—201.</a> </li>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-43809187857105539662021-03-18T23:00:00.056+00:002023-08-07T10:04:23.751+01:00Mancude rings and annulenes<p> What do the structures <b>(a)</b>, <b>(b)</b> and <b>(c)</b> have in common? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33852" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="[18]annulene (CHEBI:33852)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzojFXwJyFH2NUW1vUdM-XGZqtKQLnv617B3m7a9DmGY5MoCgK43yX3s_fWY30nZL-qcs_0ZKZ-JtFTeeDxoXtNuH-X6rL-wrzaZTSeRT3afg0e-w9U4Zm0HE-uH3Zffc-gVz22w/s0/%255B18%255Dannulene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:167642" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3,5,2,4,6-triazatriphosphinine (CHEBI:167642)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzRJ52mKx_PqBoa0BACDNwrcIHHBVihb2KQP6g46l3lcoMvy8QHmMlNIWlKoJ-hldFe5Lb5BURW2rm_qqRaRkIomsX1cInacc-uuI5v1ikbyp1AzGEznOGdx8NVzg5IGyFUL-Cbg/s0/cyclotriphosphazene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30856" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="thiophene (CHEBI:30856)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiiYRBqMCDc0t0sc-UCJhIovOMmf6R9otDLfBcukmBED_dOceiuLcvwenkgkOcQjiwwoUGrQvFzZZHHjRX0hgmYqOj7ASsbkP36NGtE8ctj9TBVHYkKsp5pOEp5y8Vw4-cWL_GEhw/s0/thiophene.png" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th> <th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> [18]annulene <br />
cyclooctadeca-1,3,5,7,9,11,13,15,17-nonaene (<a href="http://en.wikipedia.org/wiki/Preferred_IUPAC_name" target="_blank" title="Preferred IUPAC name in Wikipedia"><i>PIN</i></a>) </li>
<li> 1,3,5,2,4,6-triazatriphosphinine </li>
<li> thiophene </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Well, <a href="http://lothruput.blogspot.com/2012/10/professor-awakens-you-fail.html" target="_blank" title="professor awakens, you fail @ low-throughput">it is obvious</a> that they all are rings. Also, apart from hydrogens in <b>(a)</b> and <b>(c)</b>, they have no side chains. Otherwise, they are quite different. The structure <b>(a)</b> is a hydrocarbon. The ring <b>(b)</b> is purely inorganic while <b>(c)</b> is an organic heterocycle. What else? </p>
<p> You can see that in all these structures single bonds alternate with double bonds. Ring systems like this are referred to as <a href="http://goldbook.iupac.org/terms/view/M03695" target="_blank" title="mancude-ring systems in Gold Book"><i>mancude</i></a>, which is an abbreviation of the “<b>ma</b>ximum number of <b>n</b>on-<b>cu</b>mulative <b>d</b>ouble bonds”. </p>
<a name='more'></a>
Let’s have a look at the structure <b>(a)</b> known as [18]annulene. The term <i>annulene</i>, from Latin <a href="http://en.wiktionary.org/wiki/annulus" target="_blank" title="annulus"><i>annulus</i></a> “ring” and ‘ene’ for double bond, was coined in the early 1960s by Franz Sondheimer and Reuven Wolovsky [<a href="#Sondheimer_and_Wolovsky_1962" title="Sondheimer and Wolovsky (1962)">1</a>, <a href="#Sondheimer_1971" title="Sondheimer (1971)">2</a>]. <a href="http://goldbook.iupac.org/terms/view/A00368" target="_blank" title="annulenes in Gold Book">Gold Book</a> defines annulenes as
<blockquote> Mancude monocyclic hydrocarbons without side chains of the general formula C<sub><i>n</i></sub>H<sub><i>n</i></sub> (<i>n</i> is an even number) or C<sub><i>n</i></sub>H<sub><i>n</i>+1</sub> (<i>n</i> is an odd number). </blockquote>
<center>
<table>
<tr><th>Order</th> <th align="left">Formula</th> <th align="center">Structure</th> <th align="center">PIN</th> <th align="left">Annulene name</th> <th align="left">Group formula</th> <th align="left">Group name</th></tr>
<tr><th><p></p></th></tr>
<tr><th>3</th> <td align="center">C<sub>3</sub>H<sub>4</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51205" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclopropene (CHEBI:51205)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiB4P0U4I-Ytg9UvZ7fwMSn9IVDR48Lv05bI4UKOjwTAelcyNYLzHDbPdC0G61uJNxaD34BaBJPreN6XX74ONLD8pU0Lz_ZdHo7BDyNGfkZkV5obFlGQqubFzf2N-Q_pvDnBCONgw/w200-h200/cyclopropene.png" width="100" /></a></td> <td>cyclopropene</td> <td>[3]annulene</td> <td align="center">–C<sub>3</sub>H<sub>3</sub></td> <td> cycloprop-1-en-1-yl <br /> cycloprop-2-en-1-yl </td> </tr>
<tr><th>4</th> <td align="center">C<sub>4</sub>H<sub>4</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33657" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclobuta-1,3-diene (CHEBI:33657)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEib7CKNmez22Fln_UZ23nbPUdpDgH-RCNrfsGstZUEnfpObRiyX0__t-_HO8_mIieRsIj5tq1x3tvTsFATm4a-Mot8-X5DVoFvT-3yRiT8eFYQpPvaaQITb53jnQQOxB0_GqFcVYQ/w200-h200/cyclobuta-1%252C3-diene.png" width="100" /></a></td> <td>cyclobuta-1,3-diene</td> <td>[4]annulene</td> <td align="center">–C<sub>4</sub>H<sub>3</sub></td> <td>cyclobuta-1,3-dienyl</td> </tr>
<tr><th>5</th> <td align="center">C<sub>5</sub>H<sub>6</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30664" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclopentadiene (CHEBI:30664)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjqMI4nFJVvyPcR7_3Q-UqLKaOKx9mOxk36w2zKMGNxK99UGP_0j-qpQJOiZbR4BguLqhbCF3TSKL3_FLHZMlwK4m_l4g7vcbjeMDj2Xwp2d_5l9uds6SdmB-Qm01jHm2Pq37X7bw/w200-h200/cyclopentadiene.png" width="100" /></a></td> <td>cyclopenta-1,3-diene</td> <td>[5]annulene</td> <td align="center">–C<sub>5</sub>H<sub>5</sub></td> <td>cyclopenta-1,3-dien-1-yl <br /> cyclopenta-2,4-dien-1-yl</td> </tr>
<tr><th>6</th> <td align="center">C<sub>6</sub>H<sub>6</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16716" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="benzene (CHEBI:16716)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgySQ8lNEPPxF4I6hi7bLwd6tiAniNvOGE5O5FrKhLQse_GRa5z6wBIy4LyhoD-CsezpkY5gEsHCynx42Mjg0Khf-ny3MgFPRoe8HmB0xX20hNuBYRah6u0PqIVy72Bfi2KM0ygAQ/s200/benzene.png" width="100" /></a></td> <td>benzene</td> <td>[6]annulene</td> <td align="center">–C<sub>6</sub>H<sub>5</sub></td> <td>phenyl</td> </tr>
<tr><th>7</th> <td align="center">C<sub>7</sub>H<sub>8</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37519" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclohepta-1,3,5-triene (CHEBI:37519)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhY0lNEYl1F-p0SEMIq2fNQ_OXhwM4YKxB9C_ldN2Phv4_cwTzzOiqRkzsmxjKtLa3s7gygz1P_Rv88R376gu0iD3NrR60wc_uufuObAKNHiHdta5RNEdzgosWHSdFtOJ2wCrfXEg/w200-h200/cyclohepta-1%252C3%252C5-triene.png" width="100" /></a></td> <td>cyclohepta-1,3,5-triene</td> <td>[7]annulene</td> <td align="center">–C<sub>7</sub>H<sub>7</sub></td> <td>cyclohepta-1,3,5-trien-1-yl <br /> cyclohepta-2,4,6-trien-1-yl</td> </tr>
<tr><th>8</th> <td align="center">C<sub>8</sub>H<sub>8</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47034" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="[8]annulene (CHEBI:47034)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1mAhm6_zJCss-PiI4uE53wDyyMXZrxcjeH7cus5irhpIBlXskvWQ4eXXik0VlPobTmbdQr3zWCl8mDe1RFQCB1cd1S_pre_ECtTDhAhgd9EeNAOSPHbbsCSJZjkkYLUeGA49SKg/s0/%255B8%255Dannulene.png" width="100" /></a></td> <td>cycloocta-1,3,5,7-tetraene </td> <td>[8]annulene</td> <td align="center">–C<sub>8</sub>H<sub>7</sub></td> <td>cycloocta-1,3,5,7-tetraenyl</td> </tr>
</table></center>
<p> And so on. </p>
<p> As the rings grow in size, or rather as the number of double bonds in the ring increases, the <a href="http://metallome.blogspot.com/2021/03/alicyclic-monocycles.html" target="_blank" title="Alicyclic monocycles @ this blog">cycloalkane</a>-based systematic names progressively become more and more cumbersome. One can see that the name like cycloocta-1,3,5,7-tetraene, while easily analysable as “cyclic hydrocarbon containing eight carbon atoms with four double bonds at positions 1, 3, 5 and 7”, fails miserably to convey its most conspicuous structural feature, that is, its fourfold symmetry. It is so much better to name a ring with <i>n</i> carbon atoms [<i>n</i>]annulene. Even though <a href="http://goldbook.iupac.org/terms/view/A00368" target="_blank" title="annulenes in Gold Book">Gold Book</a> reserves this method for rings with <i>n</i>≥7, I don’t see why we can’t use it for lower annulenes. </p>
<p> The general method of naming substituent groups (other than derived from <a href="http://metallome.blogspot.com/2021/02/unbranched-hydrocarbons.html" target="_blank" title="Carbon chains @ this blog"><i>n</i>-alkanes</a> and cycloalkanes) requires to cite the attachment point locant number, including ‘1’ [<a href="#Red_Book_2005" title="Red Book (2005)">3</a>, p. 204]. This makes sense for monovalent groups derived from <i>odd</i>-numbered annulenes. There are two types of attachment points, viz. <b>(I)</b> <i>sp</i><sup>2</sup> carbon (>C=) and <b>(II)</b> <i>sp</i><sup>3</sup> carbon (>CH–); since both are assigned the locant number ‘1’, renumbering of locants for double bonds may be required. For example, the groups derived from cyclopenta-1,3-diene are named cyclopenta-1,3-dien-1-yl and cyclopenta-2,4-dien-1-yl (not cyclopenta-1,3-dien-2-yl), for type <b>I</b> and <b>II</b> attachment points, respectively. But for monovalent groups derived from <i>even</i>-numbered annulenes there is no real need to cite the attachment point locant since <i>all</i> attachment points are of the type <b>I</b>. For instance, the name cyclobuta-1,3-dienyl is completely unambiguous, so no need to call it cyclobuta-1,3-dien-1-yl. Even better, we can use ‘[<i>n</i>]annulenyl’ to name even-numbered groups<sup><a href="#Footnote_*" title="Footnote *">*</a></sup>.</p>
<p> Now [6]annulene is a special case. Not only its PIN is ‘benzene’ (not <strike>cyclohexa-1,3,5-triene</strike>), but also the derived monovalent group is called phenyl (not <strike>benzenyl</strike>). This, you may recall, is an example of <a href="http://metallome.blogspot.com/2021/01/irregularity-and-suppletion.html" target="_blank" title="Irregularity and suppletion @ this blog">suppletion</a>. Benzene is so far the only chemical structure to be assigned the <a href="http://metallome.blogspot.com/2009/04/chemical-symbols-in-unicode.html" target="_blank" title="Chemical symbols in Unicode @ this blog">Unicode symbol</a> — in fact, <i>two</i> Unicode symbols: the <a href="https://en.wikipedia.org/wiki/August_Kekul%C3%A9" target="_blank" title="August Kekulé in Wikipedia">Kekulé</a> structure <span style="font-size: medium;">⌬</span> and delocalised <span style="font-size: medium;">⏣</span>. </p>
<p> There are three possible divalent groups derived from benzene: </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35448" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,2-phenylene group (CHEBI:35448)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHkROtpPmQ_UhoLLTnvIkVtcsgMiahAyA4wtg0ohAngbu7KqTDMQZMb7P6O_QGxy0ABOq4AKkxbvyriQZyNAucSVY4xz_8h1WFpn5wgepDurExSLL9yH7k1O4oA4CjVlsa8pXllg/s0/o-phenylene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35449" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,3-phenylene group (CHEBI:35449)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOq73cmDyyAiYNDmvdgvTak9sub6vnXAwaIP8COp25k_0ROi6C1Wp9iSQLk4CZsvsbCQ3mHkPdtliZnNu8eK672vC5UFKBn84PcV7DHUnMLGDaOs3rSZgNiKaGW00IBRWpkIP7kQ/s0/m-phenylene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:35450" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,4-phenylene group (CHEBI:35450)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6d6qXjRUJRDzKRQE7MBOtNg7Nty6PHmS8ZO0WPOx3tmNSGPlE4FcSuFcz3SMLtYMi0P_Pcg1kdmrez2NwDnaYIwrG1ut06Hxy0R9eLRG7uj1Ok7hY8F_hxQYRH95WsGBqAd1Vig/s0/p-phenylene.png" /></a></td>
</tr>
<tr><th align="center">(d)</th> <th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="4" type="a">
<li> 1,2-phenylene </li>
<li> 1,3-phenylene </li>
<li> 1,4-phenylene </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Benzene is the archetypical <a href="http://goldbook.iupac.org/terms/view/A00441" target="_blank" title="aromatic in Gold Book">aromatic</a> molecule. According to <a href="http://en.wikipedia.org/wiki/Aromaticity#The_term_%22aromatic%22" target="_blank" title="Aromaticity: The term “aromatic” in Wikipedia">Wikipedia</a>, </p>
<blockquote> The first known use of the word “aromatic” as a chemical term — namely, to apply to compounds that contain the phenyl group — occurs in an article by <a href="http://en.wikipedia.org/wiki/August_Wilhelm_von_Hofmann" target="_blank" title="August Wilhelm von Hofmann in Wikipedia">August Wilhelm Hofmann</a> in 1855. </blockquote>
<p> Yes, that same Hofmann who <a href="http://metallome.blogspot.com/2021/02/hofmanns-footnote.html" target="_blank" title="von Hofmann’s footnote @ this blog">named alkanes</a> practically as we know them now. Curiously, in his paper [<a href="#Hofmann_1856" title="Hofmann (1856)">4</a>] he mentions “aromatic acids”<sup><a href="#Footnote_†" title="Footnote †">†</a></sup> as if the term needed no explanation whatsoever. </p>
<p> Not all annulenes are aromatic. Apart from benzene, [14]-, [18]-, and [22]annulenes are shown to be aromatic, while [4]annulene is <a href="http://en.wikipedia.org/wiki/Antiaromaticity" target="_blank" title="Antiaromaticity in Wikipedia"><i>antiaromatic</i></a>. On the other hand, both cyclopentadienide <b>(g)</b> and <a href="http://en.wikipedia.org/wiki/Tropylium_cation" target="_blank" title="Tropylium cation in Wikipedia">tropylium</a> <b>(h)</b> ions have six π-electrons and thus are isoelectronic with benzene. Their respective PINs, however, slavishly describe the structures in terms of localised bonds and charges. On top of that, the carbon atom that formally acquires a charge is assigned the locant number ‘1’, thus prompting renumbering of double bond locants: cyclopenta-1,3-diene → cyclopenta-2,4-dienide; cyclohepta-1,3,5-triene → cyclohepta-2,4,6-trienylium. The alternative names [5]annulenide and [7]annulenium are much shorter. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36767" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclopentadienide (CHEBI:36767)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1qsRxS3FwUomKVSouRavNuvuaWrckgdwn67JZSRix9dk_JWSSEHD1UWCrEYvvp3fK8CrNaFfMuQoZXMfcnPuFmFHlfalUOoGkbHh9XQ2-EANPUCV_EPhFPavr3lUez_ZZDRY6ug/w200-h200/cyclopentadienide.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:48079" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclohepta-2,4,6-trienylium (CHEBI:48079)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfqdqIp1eSlTMikI25bcUWMpsrMHjFZS5-d7xyzTdprJwvSUG6JuIOoKyHdhObiVFuddBCOzY4-H1gN0dO3bCZb_M-GqCWn8s-MbSzOWbqf2zdpUykdHhyphenhyphenOHQAC_9R-4wOOS4rSQ/w200-h200/cyclohepta-2%252C4%252C6-trienylium.png" width="200" /></a></td>
</tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> C<sub>5</sub>H<sub>5</sub><sup>−</sup> <br />
cyclopenta-2,4-dienide (<i>PIN</i>) <br />
[5]annulenide </li>
<li> C<sub>7</sub>H<sub>7</sub><sup>+</sup> <br />
cyclohepta-2,4,6-trienylium (<i>PIN</i>) <br />
tropylium (<i>trivial</i>) <br />
[7]annulenium </li>
</ol>
</td>
</tr>
</table>
</center>
<p> <a href="http://goldbook.iupac.org/terms/view/A00435" target="_blank" title="arenes in Gold Book">Gold Book</a> defines arenes as </p>
<blockquote> Monocyclic and polycyclic aromatic hydrocarbons. </blockquote>
<p> Benzene is often thought of as the simplest arene, although the simpler <a href="http://en.wikipedia.org/wiki/Cyclopropenium_ion" target="_blank" title="Cyclopropenium ion in Wikipedia">cyclopropenylium</a> C<sub>3</sub>H<sub>3</sub><sup>+</sup> and cyclopentadienide C<sub>5</sub>H<sub>5</sub><sup>−</sup> ions are also aromatic hydrocarbons. In any case, benzene is the simplest (neutral) arene molecule.</p><p> In higher annulenes, an additional problem arises as there could be quite a number of <a href="http://en.wikipedia.org/wiki/Cis%E2%80%93trans_isomerism" target="_blank" title="Cis–trans isomerism in Wikipedia"><i>cis</i>/<i>trans</i> isomers</a>. For instance, the variants on [18]annulene <b>(a)</b> theme include structures <b>(g)</b> and <b>(h)</b>, with accordingly unwieldy systematic names. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37520" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(1E,3Z,5E,7E,9Z,11E,13E,15Z,17E)-cyclooctadeca-1,3,5,7,9,11,13,15,17-nonaene (CHEBI:37520)"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEifnjAETEx3k1bf6eDyxG7laZ4mJjmM-xcifbz-lg9LOnRzDHtyZMARJTK6P08I_Nlw5BvW5c7b-33LhyW_erXKPq6f3izT9pZgMbfqVhFTdWY6BHcUhydFv4dBlSco1nsBbmAtmg/w200-h200/%255B18%255Dannulene.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37521" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="(1Z,3E,5E,7E,9Z,11Z,13E,15E,17E)-cyclooctadeca-1,3,5,7,9,11,13,15,17-nonaene (CHEBI:37521)"><img border="0" data-original-height="500" data-original-width="500" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJUipjS2lXIAGlcaZMxay48s9mXntp3rD6-pROlPJXBwVNoZtXmaDV1cuDZ0Mb9nzA2vphG252vkGESwRzKrbcWYWKJbCnpYr10t9gYWa6Pw-0dnzpUYTRfq_7-XrzZOK6SjXwuQ/w200-h200/%255B18%255Dannulene.png" width="200" /></a></td>
</tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> (1<i>E</i>,3<i>Z</i>,5<i>E</i>,7<i>E</i>,9<i>Z</i>,11<i>E</i>,13<i>E</i>,15<i>Z</i>,17<i>E</i>)-cyclooctadeca-1,3,5,7,9,11,13,15,17-nonaene </li>
<li> (1<i>Z</i>,3<i>E</i>,5<i>E</i>,7<i>E</i>,9<i>Z</i>,11<i>Z</i>,13<i>E</i>,15<i>E</i>,17<i>E</i>)-cyclooctadeca-1,3,5,7,9,11,13,15,17-nonaene </li>
</ol>
</td>
</tr>
</table>
</center>
<a name="Footnote_*"></a>
<a name="Footnote_†"></a>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> We also can use ‘[<i>n</i>]annulenyl’ for odd-numbered groups if we can’t (or don’t want to) specify attachment points. </td>
</tr>
<tr><td valign="top">†</td>
<td> Hofmann’s list of “monobasic aromatic acids” [<a href="#Hofmann_1856" title="Hofmann (1856)">4</a>] includes <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30746" target="_blank" title="benzoic acid (CHEBI:30746)">benzoic acid</a>, toluylic acid (now <a href="http://en.wikipedia.org/wiki/Toluic_acid" target="_blank" title="Toluic acid in Wikipedia">toluic acid</a>) and cuminic acid (now <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:23412" target="_blank" title="cumic acid (CHEBI:23412)">cumic acid</a>), while “bibasic” ones include <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29069" target="_blank" title="phthalic acid (CHEBI:29069)">phthalic acid</a>, <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15702" target="_blank" title="terephthalic acid (CHEBI:15702)">terephthalic acid</a> and the titular “<a href="http://www.numericana.com/arms/hofmann.htm" target="_blank" title="August Wilhelm von Hofmann (1818-1892) @ numericana.com">insolinic acid</a>” which could be either methylterephthalic acid, 5-methylisophthalic acid (<a href="https://en.wikipedia.org/wiki/Uvitic_acid" target="_blank" title="Uvitic acid in Wikipedia">uvitic acid</a>) or 4-methylphthalic acid. </td></tr>
</table>
<h4> References </h4>
<ol>
<a name="Sondheimer_and_Wolovsky_1962"></a>
<li> Sondheimer, F. and Wolovsky, R. (1962) Unsaturated macrocyclic compounds. XXI. The synthesis of a series of fully conjugated macrocyclic polyene-polyynes (dehydro-annulenes) from 1,5-hexadiyne. <a href="https://doi.org/10.1021/ja00861a028" target="_blank" title="Sondheimer & Wolovsky (1962) J. Am. Chem. Soc. 84, 260-269."><i>Journal of the American Chemical Society</i> <b>84</b>, 260—269</a>. </li>
<a name="Sondheimer_1971"></a>
<li> Sondheimer, F. (1971) Recent progress in the annulene field. <a href="http://doi.org/10.1351/pac197128020331" target="_blank" title="Sondheimer, F. (1971) Pure Appl. Chem. 28, 331-354."><i>Pure and Applied Chemistry</i> <b>28</b>, 331—354</a>. </li>
<a name="Red_Book_2005"></a>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
<a name="Hofmann_1856"></a>
<li> Hofmann, A.W. (1856) On insolinic acid. <a href="http://doi.org/10.1098/rspl.1856.0002" target="_blank" title="Hofmann, A.W. (1856) Proc. R. Soc. 8, 1-3."><i>Proceedings of the Royal Society</i> <b>VIII</b>, 1—3</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-6246425892606977152021-03-02T12:00:00.008+00:002023-08-07T10:05:32.880+01:00Alicyclic monocycles<p> Now let us have a look at monocyclic hydrocarbons, starting with <a href="http://en.wikipedia.org/wiki/Cycloalkane" target="_blank" title="Cycloalkane in Wikipedia"><i>cycloalkanes</i></a>. By the way, I think this term is a bit misleading: cycloalkanes indeed contain cycles but are <i>not</i> <a href="http://goldbook.iupac.org/terms/view/A00222" target="_blank" title="alkanes in Gold Book">alkanes</a> because these latter, by definition, are acyclic. Gold Book defines <a href="http://goldbook.iupac.org/terms/view/C01497" target="_blank" title="cycloalkanes in Gold Book">cycloalkanes</a> as “saturated monocyclic hydrocarbons (with or without side chains)”, where “side chains” are <a href="http://goldbook.iupac.org/terms/view/A00228" target="_blank" title="alkyl groups in Gold Book">alkyl groups</a>. The general molecular formula of cycloalkanes, with or without side chains, is C<sub><i>n</i></sub>H<sub>2<i>n</i></sub>. I wish there was an elegant collective term for cycloalkanes-with-no-side-chains, or unsubstituted cycloalkanes, because only this subset of cycloalkanes can be used as <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">parent hydrides</a> in systematic organic nomenclature; I am not aware of any. Here, I will refer to unsubstituted cycloalkanes as ‘cycloalkane parents’<sup>*</sup>. </p>
<a name='more'></a>
<p> Using the <a href="http://metallome.blogspot.com/2021/01/chains-and-rings.html" target="_blank" title="Chains and rings @ this blog">graph theory language</a>, we can say that every cycloalkane is a (hydrogen-depleted) <i>unicyclic graph</i> or <i>1-tree</i> in which all vertices are carbon atoms, while cycloalkane parents are <a href="http://en.wikipedia.org/wiki/Cycle_graph" target="_blank" title="Cycle graph in Wikipedia"><i>cycle graphs</i></a>. </p>
<center>
<table>
<tr><th>Order</th> <th align="left">Formula</th> <th align="center">Structure</th> <th align="left">Name</th> <th align="left">Group formula</th> <th align="left">Group name</th></tr>
<tr><th><p></p></th></tr>
<tr><th>3</th> <td align="center">C<sub>3</sub>H<sub>6</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30365" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclopropane (CHEBI:30365)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgmW4WWCTdKw-EA4q6cCXW9QRvZGMUyAKnvWKc6z_GkGExbUXPEPnuXkmzyHX5Gf4t3qePqWK5AoINNf7tHRPRzXsiH3LVVZ7X_g8Mr062DAjB5jyvceTjBdxYwWEZI-RxZCQP9FA/s0/cyclopropane.png" width="100" /></a></td> <td>cyclopropane</td> <td align="center">–C<sub>3</sub>H<sub>5</sub></td> <td>cyclopropyl</td> </tr>
<tr><th>4</th> <td align="center">C<sub>4</sub>H<sub>8</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30377" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclobutane (CHEBI:30377)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfbrRkzQYqLuW5zhPG5x0Dse1I2VJIrEZ9zc_LSfRSkaj6vZ30EQ09mjhFaMhu0tnpa73fU8aeSaY7cwv1uVmE29eviwa_TsAqpvGCtLaWZVqvBk4lQKBxM-R7jZq7TtayU6_OHg/s0/cyclobutane.png" width="100" /></a></td> <td>cyclobutane</td> <td align="center">–C<sub>4</sub>H<sub>7</sub></td> <td>cyclobutyl</td> </tr>
<tr><th>5</th> <td align="center">C<sub>5</sub>H<sub>10</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:23492" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclopentane (CHEBI:23492)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSSM2ltIgqWXt7E8VRq54aCvPJGMUxpVftnPI2IyIyqNGwPudJ6nLXnIRa8tzE5ztI9d4ukP3_TtfwLxcY9G2Tp1AcsXHKxENgkwD83cJLgyWEXwyGq79oyptQYoiqAcfm7t38lA/s0/cyclopentane.png" width="100" /></a></td> <td>cyclopentane</td> <td align="center">–C<sub>5</sub>H<sub>9</sub></td> <td>cyclopentyl</td> </tr>
<tr><th>6</th> <td align="center">C<sub>6</sub>H<sub>12</sub></td> <td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29005" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclohexane (CHEBI:29005)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPJOhSxBcicwYwYWtSg1ubhGtS51UFB3_LHf2SQvZL1bpxIiBQ_5LqAAh4vaO9fzCbvs9-1NQHy6QWukJuEohRRNwJkw0oaE1UmDe0mqWyl4V_SRQK0MDGWyEb7AntAIWKU94U-g/s1600/cyclohexane.png" width="100" /></a></td> <td>cyclohexane</td> <td align="center">–C<sub>6</sub>H<sub>11</sub></td> <td>cyclohexyl</td> </tr>
<tr><th>7</th> <td align="center">C<sub>7</sub>H<sub>14</sub></td> <td><a href="http://chem.nlm.nih.gov/chemidplus/number/291-64-5" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cycloheptane (CAS 291-64-5)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRx1heNGigY1SifwFRGeYGmIX2DGPnpyJ3iqH97I4Hvkev6aZYZUWjSjLxGD4XqVJV0swbiLFHWYhoYKIklD0kFSijjftWP0qxaTbYU2OUI-LdJTW9QaXXIlrdEkjcDpUGj07MNA/s0/cycloheptane.png" width="100" /></a></td> <td>cycloheptane</td> <td align="center">–C<sub>7</sub>H<sub>13</sub></td> <td>cycloheptyl</td> </tr>
<tr><th>8</th> <td align="center">C<sub>8</sub>H<sub>16</sub></td> <td><a href="http://chem.nlm.nih.gov/chemidplus/number/292-64-8" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclooctane (CAS 292-64-8)"><img border="0" data-original-height="200" data-original-width="200" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgO2ClUqpXbqoMnyou_kZxHFhHj_FbrrBeFQ3SfbBEg55tlx5upnnxhdQrpNWCfNEcAJ9bpuc4KruQPvIlT0vwDo1aS3mvOu_1QLpOQiFxBJ5OZrMUN8ZM7BHBcaZmK5xEs_bPX-A/s0/cyclooctane.png" width="100" /></a></td> <td>cyclooctane</td> <td align="center">–C<sub>8</sub>H<sub>15</sub></td> <td>cyclooctyl</td> </tr>
</table></center>
<p> And so on. </p>
<p> The names of cycloalkanes, just like those of alkanes, only <i>imply</i> their carbon and hydrogen composition, which again could be contrasted with the names of their silicon analogues. For example, the name ‘<a href="http://en.wikipedia.org/wiki/Cyclopentasilane" target="_blank" title="Cyclopentasilane in Wikipedia">cyclopentasilane</a>’ is easily analysed in terms of combining forms ‘cycl(o)’ = cyclic, ‘pent(a)’ = five, ‘sil’ = silicon and ‘an’ = saturated hydride, i.e. “cyclic hydride containing five silicon atoms”. On the other hand, ‘cyclopentane’ simply means “cyclic saturated hydride containing five non-hydrogen atoms”. Also, like <i>n</i>-alkyl group names, the cycloalkyl group names lack the ‘an’ bit: cyclopropane → cyclopropyl (not <strike>cyclopropanyl</strike>), cyclobutane → cyclobutyl (not <strike>cyclobutanyl</strike>), cyclopentane → cyclopentyl (not <strike>cyclopentanyl</strike>), etc., whicle their silicon analogues will retain ‘an’ as in cyclopentasilane → cyclopentasilanyl. </p>
<p> Since there are no terminal vertices, no locants are needed for a <i>single</i> cycloalkane parent modification, be it a substitution or unsaturation. For example, we name the structure <b>(a)</b> methylcyclohexane, not 1-methylcyclohexane; the structure <b>(b)</b> cyclohexene, not cyclohex-1-ene; and <b>(c)</b> cycloundecyne, not cycloundec-1-yne: </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:165745" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="methylcyclohexane (CHEBI:165745)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEisF8w5rCpDwuN0joJlbipf5DBGmqOU66bxRLnS8D2ZIJ5NviH_2VRlYvSMAlcI8C-v4-OCThzxicISdSeJSBrHyHTg72r2fZmm4-FlwcE-AoBWXq18bXrWUAb50Qfu9680SMaQKA/s0/methylcyclohexane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36404" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclohexene (CHEBI:36404)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg61quVAqgGR0g5LjHjFKo0DujlLXUF4QsD6-eGiEW1S8w7ZGDjS5Fa9axGVE2Gaa4NBtRCpNNKgize8Te36_evELjuEAx3uHW6P8b2zdKoiRSHnOW2LVnvZhoM5YtFFAnqno4NQg/s0/cyclohexene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37818" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cycloundecyne (CHEBI:37818)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHgFmXFchyvwfQArTjoyeWFba5VSekVuX4RgcXOtTbMHKoc9kfqLVq7ioPft-LjDBnqwURxDMufy-sMAX_NE8dvA9HkWUKBg-MUWsbffp4WecvM89vKDbsKQZwVBcte2Mx6xYSPw/s0/cycloundecyne.png" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th> <th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> methylcyclohexane </li>
<li> cyclohexene </li>
<li> cycloundecyne </li>
</ol>
</td>
</tr>
</table>
</center>
<p> As soon as <i>another</i> modification is introduced into a ring though, we do need locants to differentiate between isomers. For instance, the structure <b>(d)</b> is named 1,4-dimethylcyclohexane (because both 1,2-dimethylcyclohexane and 1,3-dimethylcyclohexane also exist); <b>(e)</b> is called cyclohexa-1,3-diene (both <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37612" target="_blank" title="cyclohexa-1,2-diene (CHEBI:37612)">cyclohexa-1,2-diene</a> and <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37611" target="_blank" title="cyclohexa-1,4-diene (CHEBI:37611)">cyclohexa-1,4-diene</a> are also possible); and <b>(f)</b>, cyclooctadeca-1,3,5,7,9,11,13,15,17-nonayne<sup>†</sup>. </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:165732" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1,4-dimethylcyclohexane (CHEBI:165732)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjIYDzFq_6JDr86E2QmE8OXbtJGNkhdaAABd0u7cgt1ETjHrkuEmMoWScVTVu4o19o8wE5Huq3AZxweZDdKIpGbbfmSncI4-r4xz52qlIEcqCteTqrTP7nYK6KgLHyFQWbjinRDJQ/s0/1%252C4-dimethylcyclohexane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37610" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclohexa-1,3-diene (CHEBI:37610)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEheqZzIpp6exwKQWBbEgDsnNEpOD_otza82oNAzaj60hJNcUcaYQmMcE8iuupkK0yqXoutYol9hlpN8D7cLasXVsIOx4PkDFoiafXVOX50Q25o9jRvu_0AdP81O0Sx6XdHNR16F0g/s0/cyclohexa-1%252C3-diene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:146233" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclo[18]carbon (CHEBI:146233)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoSPrXDPqGcUWO97rctf-oPph3lXNy9eg9Wh-7c87PxhJef6y-t266-T8Z1PTnctMrtD4-FiIhia7BaTJp9Kfa2VS5EovBLw9oMhR0LPQeS-2JKxq17BSDd0X2oMfmh3wlMNaYxg/s0/cyclo%255B18%255Dcarbon.png" /></a></td>
</tr>
<tr><th align="center">(d)</th> <th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="4" type="a">
<li> 1,4-dimethylcyclohexane </li>
<li> cyclohexa-1,3-diene </li>
<li> cyclo[18]carbon (<i>trivial</i>) <br />
cyclooctadeca-1,3,5,7,9,11,13,15,17-nonayne (<i>substitutive</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Speaking about unsaturation: according to <a href="http://goldbook.iupac.org/terms/view/C01497" target="_blank" title="cycloalkanes in Gold Book">Gold Book</a>, </p>
<blockquote> Unsaturated monocyclic hydrocarbons having one endocyclic double or one triple bond are called cycloalkenes and cycloalkynes, respectively. Those having more than one such multiple bond are cycloalkadienes, cycloalkatrienes, etc. The inclusive terms for any cyclic hydrocarbons having any number of such multiple bonds are cyclic olefins or cyclic acetylenes. </blockquote>
<p> Nothing specific is said about the side chains, nevertheless it is understood that unsaturation <i>outside</i> the ring does not convert a cycloalkane into a cycloalkene or cycloalkyne. Thus, the structure <b>(g)</b> most likely is a cycloalkene while <b>(h)</b> definitely isn’t one. But what is it? </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:48695" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="4-(1-methyleneallyl)-1,5,5-trimethylcyclopentene (CHEBI:48695)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyPSO9t_ZXy4Z_R7l-jtka0jPneQbjeV7K8CB6LgvfXGlsvCzUxIxFt-ELLOh7BO_04hWbTHSka3JGdXW92aBEF9me8bksezdLHsBsL_O4Te2TSah-yYTWA0vbRSB-79SYA_rX5w/s0/4-%25281-methyleneallyl%2529-1%252C5%252C5-trimethylcyclopentene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:131418" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1-methylidene-2-(pent-4-en-1-yl)cyclopropane (CHEBI:131418)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj4Fp5GrAItx6VSF99mhkO7ZLQG7od3mPCkWlAa1o9u420EMMtNhgfwxNM8grgje5LV0WKpKMNMRNinn9W1IGd1jJdlr1INXt29q6u5kIrpV_6_fOjqcsxKQE_ZxlCcbriySN_2Bg/s0/1-methylidene-2-%2528pent-4-en-1-yl%2529cyclopropane.png" /></a></td>
</tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> 4-(buta-1,3-dien-2-yl)-1,5,5-trimethylcyclopentene </li>
<li> 1-methylidene-2-(pent-4-en-1-yl)cyclopropane </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Gold Book defines <a href="http://goldbook.iupac.org/terms/view/A00216" target="_blank" title="alicyclic compounds in Gold Book">alicyclic compounds</a> as </p>
<blockquote> Aliphatic compounds having a carbocyclic ring structure which may be saturated or unsaturated, but may not be a <a href="http://en.wikipedia.org/wiki/Benzenoid" target="_blank" title="Benzenoid in Wikipedia">benzenoid</a> or other aromatic system. </blockquote>
<p> The second part of the definition appears to be redundadnt since <a href="http://goldbook.iupac.org/terms/view/A00217" target="_blank" title="aliphatic compounds in Gold Book">aliphatic compounds</a> are already said to be </p>
<blockquote> Acyclic or cyclic, saturated or unsaturated carbon compounds, excluding aromatic compounds. </blockquote>
<p> Nothing prevents alicyclic structures from having <i>more</i> than one ring provided they are not aromatic; however, we’ll leave polycyclic structures for another time. I suppose ‘alicyclic monocycles’ or ‘monoalicyclic structures’ could be an umbrella term for all structures in this post. </p>
<p> Naming monoalicyclic hydrocarbons is straightforward: <span style="background-color: gold;">rings</span> are always senior to <span style="background-color: lightblue;">chains</span> irrespectively of their length [1]. Thus, we name the structure <b>(i)</b> 1-methyl-4-(6-methyl<span style="background-color: lightblue;">heptan</span>-2-yl)<span style="background-color: gold;">cyclohexan</span>e, not 2-methyl-6-(4-methyl<span style="background-color: gold;">cyclohex</span>yl)<span style="background-color: lightblue;">heptan</span>e<sup>‡</sup>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36480" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="bisabolane (CHEBI:36480)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGSrA8nOVUwT9SY-EukCJF4PXMM7-M4WsVL3ayipRgM8sWWapnVCksEvz1ZrFHgZmNf2T3XMEUW1T00gP5W_4bQqeWN4F-EMdM35JRwH_jHaMR53FPDYLYrzOovfdpCEDxAJ_q6w/s0/bisabolane.png" /></a></td>
</tr>
<tr><th align="center">(i)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="9" type="a">
<li> bisabolane (<i>trivial</i>) <br />
1-methyl-4-(6-methylheptan-2-yl)cyclohexane (<i>substitutive</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> I came across the term ‘alkylcycloalkanes’ which explicitly refers to cycloalkanes <i>with</i> side chains; however, if we accept this term, we should reserve the use of ‘cycloalkanes’ for cycloalkane parents only. </td>
</tr>
<tr><td valign="top">†</td>
<td> Although cyclo[18]carbon <b>(f)</b> can be systematically named as a cycloalkapolyyne, it hardly qualifies to be among cyclic hydrocarbons for the simple reason that it does not have any hydrogen. </td></tr>
<tr><td valign="top">‡</td>
<td> In earlier recommendations, seniority depended on number of atoms. If there were more atoms in the chain than in the ring, the hydrocarbon name was based on the chain name [2], thus 2-methyl-6-(4-methylcyclohexyl)heptane would be preferred to 1-methyl-4-(6-methylheptan-2-yl)cyclohexane. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<li> Hellwich, K.-H., Hartshorn, R.M., Yerin, A., Damhus, T. and Hutton, A.T. (2020). Brief guide to the nomenclature of organic chemistry (IUPAC Technical Report). <a href="http://doi.org/10.1515/pac-2019-0104" target="_blank" title="Hellwich et al. (2020) Pure Appl. Chem. 92, 527-539."><i>Pure and Applied Chemistry</i> <b>92</b>, 527—539</a>.
</li>
<li> Panico, R., Powell, W.H. and Richer, J.-C. <i>A Guide to IUPAC Nomenclature of Organic Compounds (Recommendations 1993)</i>. Blackwell Science, 1993. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-73981976769046883452021-02-25T00:00:00.016+00:002023-08-07T10:06:41.872+01:00Branched hydrocarbons<p> How can we name the structure <b>(a)</b>? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:63948" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="trimethyltin (CHEBI:63948)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDHUzYwp8rDgCmXyh0RS088kfW59y-QL9j0kgHTThLnExyCIt15uNuMGY8RvwawT501sMK55COURk_HIXPW2g-goqHIHQ0eG8iLHKvkiRhyxko0zbVonwMRTljxtChMblZopVyOQ/s0/trimethyltin.png" /></a></td>
</tr>
<tr><th align="center">(a)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> [Sn(CH<sub>3</sub>)<sub>3</sub>H] <br />
hydridotrimethyltin <i>(additive)</i> <br />
trimethylstannane <i>(substitutive)</i> </li>
</ol>
</td>
</tr>
</table>
</center>
<a name='more'></a>
<p> We can give it an <a href="http://metallome.blogspot.com/2020/06/addictive-names.html" target="_blank" title="Addi(c)tive names @ this blog">additive name</a> ‘hydridotrimethyltin’. Alternatively, based on the <a href="http://metallome.blogspot.com/p/parent-names-of-mononuclear-hydrides.html" target="_blank" title="Parent names of mononuclear hydrides @ this blog">mononuclear hydride</a> stannane SnH<sub>4</sub>, we can call it ‘trimethylstannane’. Easy. </p>
<p> Now let’s replace the central tin atom with carbon, which results in the structure <b>(b)</b>:</p>
<a name="isobutane"></a>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30363" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="isobutane (CHEBI:30363)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgR49RaAeSUJkdlscCut4DEE-4cBFZOSHD0pugyu44-k21cLGDLXG1pw3ljRNVxD99i8Tre1b8GSV6Qy3Hkr5CSWeV-IaWsLP3r4jw_dhCjBhOK03iGYdgiDchRLAL1MASwoWWbew/s0/isobutane.png" /></a></td>
</tr>
<tr><th align="center">(b)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="2" type="a">
<li>CH(CH<sub>3</sub>)<sub>3</sub> <br />
isobutane <i>(trivial)</i><br />
2-methylpropane <i>(substitutive)</i></li>
</ol>
</td>
</tr>
</table>
</center>
<p> Can’t we name it trimethylmethane? Why, of course we can. You may recall a <a href="http://metallome.blogspot.com/2020/09/multiplicative-names.html" target="_blank" title="Multiplicative names @ this blog">similar substitutive name</a> for the structure <b>(c)</b>. However, as far as the naming of alkanes is concerned, a different method is used. Namely, the name is based on longest <a href="http://metallome.blogspot.com/2021/01/chains-and-rings.html" target="_blank" title="Chains and rings @ this blog">chain</a>. Using the graph theory language, if our structure is a <a href="http://en.wikipedia.org/wiki/Tree_(graph_theory)" target="_blank" title="Tree (graph theory) in Wikipedia"><i>tree</i></a> <i>G</i>, we are looking for a <i>subgraph</i> <i>G</i>′ that is the longest <a href="http://en.wikipedia.org/wiki/Path_(graph_theory)" target="_blank" title="Path (graph theory) in Wikipedia"><i>path</i></a>. In the case of <b>(b)</b> the longest chain is propane <b>(d)</b>, so the <a href="http://en.wikipedia.org/wiki/Preferred_IUPAC_name" target="_blank" title="Preferred IUPAC name in Wikipedia">preferred IUPAC name</a> (PIN) for <b>(b)</b> is 2-methylpropane. </p>
<p> I’ll tell you why I dislike this name. First, the locant ‘2’ is superfluous: there is only one way to attach methyl group to propane without converting the longest chain to butane. Second, the name does not reflect the obvious fact that there are <i>three identical groups</i> bonded to the central atom. My internal coordination chemist is not happy! </p>
<center>
<table>
<tr><td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:76212" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="triphenylmethane (CHEBI:76212)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQx71fAZWVEceNM_gscK4mabO95Av1C_HIBZhRlMqVUNwsxhF_6_Uaq6uKLNp9TyPNrmEuiIzbmUZj_m5LW9WpgI4ZLt5HwaEdIr_9e1nt-PFsDHLiL5eHoRg3KUCdmKq90j36Ww/s1600/triphenylmethane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32879" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="propane (CHEBI:32879)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFsJf6g4JSycVGdrYWd2ON_cc0ngzH3D4tYnnQehq-ZpwTrH4MbvajMj2Ka-jlcw0cv_gZkFkCFy5JbHD_CcgHVX_ya1E1i8_XZMMaHhU125aR2ixLy1Dod8MJgrvrs6DgutsJoA/s0/propane.png" /></a></td>
</tr>
<tr><th align="center">(c)</th> <th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="3" type="a">
<li> triphenylmethane (<i>substitutive</i>) <br />
1,1′,1″-methanetriyltribenzene (<i>multiplicative</i>) </li>
<li> H<sub>3</sub>C–CH<sub>2</sub>–CH<sub>3</sub> <br />
propane (<i>parent hydride</i>)</li>
</ol>
</td>
</tr>
</table>
</center>
<a name="neopentane"></a>
<p> Likewise, the only difference between the structures <b>(e)</b> and <b>(f)</b> is the central atom. So, the name tetramethylmethane for <b>(f)</b> makes every sense but, alas, is not the one recommended by IUPAC. Instead, the PIN is 2,2-dimethylpropane. I guess by now you understand why it doesn’t make me ecstatic either. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30183" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="tetramethyllead (CHEBI:30183)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3ff-b4oDfXxRdihBSNOe373FAs6Pzbk1kbRjzYzCr-PO1HCye4y5NoGjaSp9auGtdOty6v6STAdSUBcY6Xqx6X0HC6a3Cy02JT04l0aHzYvbBfKPJUnD0EaguzG2Zd2uB_w1JIw/w200-h200/tetramethyllead.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30358" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="neopentane (CHEBI:30358)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhPwQDRD4fI4KXLhotylwvswdZszVwh6WU70_IpqC6QnfuMzpAYeSd50N2mM_vSnrC43CmY-PPYvhfDtmL8hrVSZ5Ik5i65Q-gXL1I5l5aAzhXFe7RjcXJkLG8p10HYwX8DlkPNwA/s0/neopentane.png" /></a></td>
</tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> Pb(CH<sub>3</sub>)<sub>4</sub> <br />
tetramethyllead <i>(additive)</i> <br />
tetramethylplumbane <i>(substitutive)</i> </li>
<li>C(CH<sub>3</sub>)<sub>4</sub> <br />
neopentane <i>(trivial)</i><br />
2,2-dimethylpropane <i>(substitutive)</i></li>
</ol>
</td>
</tr>
</table>
</center>
<p> The reason why the current system is used is the sheer number of <a href="http://en.wikipedia.org/wiki/Alkane#Isomerism" target="_blank" title="Alkane in Wikipedia: Isomerism">alkane isomers</a>. There are only two C<sub>4</sub>H<sub>10</sub> isomers, so it’s easy enough to give them trivial names, <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37808" target="_blank" title="butane (CHEBI:37808)">butane</a> and <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30363" target="_blank" title="isobutane (CHEBI:30363)">isobutane</a>. Since butane is an <a href="http://metallome.blogspot.com/2021/02/unbranched-hydrocarbons.html" target="_blank" title="Carbon chains @ this blog"><i>n</i>-alkane</a>, it used to be called ‘<i>n</i>-butane’, just to make sure that we talk about unbranched isomer. There are three C<sub>5</sub>H<sub>12</sub> isomers, viz. <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37830" target="_blank" title="pentane (CHEBI:37830)">pentane</a> (or <i>n</i>-pentane), <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30362" target="_blank" title="isopentane (CHEBI:30362)">isopentane</a>, and <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30358" target="_blank" title="neopentane (CHEBI:30358)">neopentane</a>. For C<sub>10</sub>H<sub>22</sub>, there are 75 possible isomers; for C<sub>15</sub>H<sub>32</sub>, there are 4347 isomers; for C<sub>20</sub>H<sub>42</sub>, already 366,319 isomers [1]. Of them, only few are as beautifully symmetrical as <b>(b)</b> and <b>(f)</b>, so the longest-chain method is most logical, although it might not generate the most attractive, or even the shortest, names. For example, the structure <b>(g)</b> is named 3-ethyl-3-methyldecane, not 2,2-diethylnonane, simply because decane is longer than nonane. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:165738" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="3-methyl-3-ethyldecane (CHEBI:165738)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgerzVPLpy4WnVBgN90-y-Tu8jkwQlNFHHn6vxO_acziz67wPB0OHUO3hcqz0ReE7FKe2dJ4wBSNU2afdzfLfCzPZB0JtQftbyrH0ZZKhC2D83abez_vtQbdeOKKjscUs09-GnEeQ/s0/3-methyl-3-ethyldecane.png" /></a></td>
</tr>
<tr><th align="center">(g)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> 3-ethyl-3-methyldecane <i>(substitutive)</i></li>
</ol>
</td>
</tr>
</table>
</center>
<p> If there are two or more chains of equal length, which one has to be chosen as the main one, for nomenclature purposes? Well, there are <a href="http://www.acdlabs.com/iupac/nomenclature/79/r79_36.htm" target="_blank" title="Acyclic Hydrocarbons. Rule A-2. Saturated Branched-chain Compounds and Univalent Radicals @ ACDLabs">rules</a> for that. For instance, the structure <b>(h)</b> is named 3-ethyl-2,7-dimethyloctane, not 6-isopropyl-2-methyloctane, because of the Rule A-2.6(d) that “the chain having the least branched side chains” is the senior. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:139062" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="3-ethyl-2,7-dimethyloctane (CHEBI:139062)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh80KbDlyvNtknbO7xx95MthM_GjSpvQsLVswhu3Y7Q49GBg8kznNf5jFoMo_FFGAvDsYBiwtZNaz3V-9KdbBGXG-ZoIPROKzlhAv-s_tkUaK_YWCU7H886oQ7IV-PJzcdbtnknsA/s0/3-ethyl-2%252C7-dimethyloctane.png" /></a></td>
</tr>
<tr><th align="center">(h)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="8" type="a">
<li> 3-ethyl-2,7-dimethyloctane <i>(substitutive)</i></li>
</ol>
</td>
</tr>
</table>
</center>
<p> What about branched alkenes and other unsaturated hydrocarbons? The principle remains the same: start with the longest chain [2]. Thus, the structure <b>(i)</b> is named 3-methylideneheptane, not 2-ethylhex-1-ene<sup>*</sup>. And if there are two or more chains of equal length, there are seniority <a href="http://www.acdlabs.com/iupac/nomenclature/79/r79_53.htm" target="_blank" title="Acyclic Hydrocarbons. Rule A-3. Unsaturated Compounds and Univalent Radicals @ ACDLabs">rules</a> for that too, of different degrees of arbitrariness. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:88858" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="3-methyleneheptane (CHEBI:88858)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibmTFq8gZdCOrXQhhPifCMn6spGK1Em17QQhoxH7c109Tiz3oICtSwbjNQnK50vH5vR5wPSVIA3oJMN5YWlXKLmoZ9Tspaj926ABTWvaWTGFj8t_FJp0RGnLHPsM_a3xuIP7yQoQ/s0/3-methyleneheptane.png" /></a></td>
</tr>
<tr><th align="center">(i)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="9" type="a">
<li> 3-methylideneheptane <i>(substitutive)</i></li>
</ol>
</td>
</tr>
</table>
</center>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> In earlier recommendations, however, unsaturation was <i>senior</i> to chain length [3], thus 2-ethylhex-1-ene would be preferred to 3-methylideneheptane. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<li> Sloane, N.J.A. Number of <i>n</i>-node unrooted quartic trees; number of <i>n</i>-carbon alkanes C<sub><i>n</i></sub>H<sub>2<i>n</i>+2</sub> ignoring stereoisomers. <i>On-Line Encyclopedia of Integer Sequences</i>, sequence <a href="http://oeis.org/A000602" target="_blank" title="A000602: Number of n-node unrooted quartic trees; number of n-carbon alkanes C(n)H(2n+2) ignoring stereoisomers @ OEIS">A000602</a>.</li>
<li> Hellwich, K.-H., Hartshorn, R.M., Yerin, A., Damhus, T. and Hutton, A.T. (2020). Brief guide to the nomenclature of organic chemistry (IUPAC Technical Report). <a href="http://doi.org/10.1515/pac-2019-0104" target="_blank" title="Hellwich et al. (2020) Pure Appl. Chem. 92, 527-539."><i>Pure and Applied Chemistry</i> <b>92</b>, 527—539</a>.
</li>
<li> Panico, R., Powell, W.H. and Richer, J.-C. <i>A Guide to IUPAC Nomenclature of Organic Compounds (Recommendations 1993)</i>. Blackwell Science, 1993. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-83685369319495351302021-02-08T23:30:00.018+00:002023-08-07T10:07:51.711+01:00von Hofmann’s footnote<p> Systematic name formation in chemistry typically happens through <a href="http://en.wikipedia.org/wiki/Compound_(linguistics)" target="_blank" title="Compound (linguistics) in Wikipedia">compounding</a>, <a href="http://en.wikipedia.org/wiki/Morphological_derivation" target="_blank" title="Morphological derivation in Wikipedia">derivation</a>, or mix of both. The semantic modification of a combining form through umlaut-like vowel change as seen in <a href="http://metallome.blogspot.com/2021/02/unbranched-hydrocarbons.html" target="_blank" title="Carbon chains @ this blog">alkanes/alkenes/alkynes</a> appears to be unique. Its origin could be traced to the 1866 publication of <a href="http://en.wikipedia.org/wiki/August_Wilhelm_von_Hofmann" target="_blank" title="August Wilhelm von Hofmann in Wikipedia">August Wilhelm von Hofmann</a> [1]; I probably would never know about it if not for an illuminating blog post by Joe Dixon [2]. </p>
<p> In an <a href="http://chem125-oyc.webspace.yale.edu/125/history99/5Valence/Nomenclature/Hofmannaeiou.html" target="_blank" title="Hofmann's Proposal for Systematic Nomenclature of the Hydrocarbons “On the Action of Trichloride of Phosphorus on the Salts of the Aromatic Monamines” by A. W. Hofmann, LL.D., F.R.S., &c.- Footnote on pp. 57-58">extended footnote</a>, Hofmann proposed to call the first ten alkanes as follows: <a href="http://en.wikipedia.org/wiki/Methane" target="_blank" title="Methane in Wikipedia">methane</a>, <a href="http://en.wikipedia.org/wiki/Ethane" target="_blank" title="Ethane in Wikipedia">ethane</a>, <a href="http://en.wikipedia.org/wiki/Propane" target="_blank" title="Propane in Wikipedia">propane</a>, quartane, quintane, sextane, septane, <a href="http://en.wikipedia.org/wiki/Octane" target="_blank" title="Octane in Wikipedia">octane</a>, <a href="http://en.wikipedia.org/wiki/Nonane" target="_blank" title="Nonane in Wikipedia">nonane</a> and <a href="http://en.wikipedia.org/wiki/Decane" target="_blank" title="Decane in Wikipedia">decane</a>.
<a name='more'></a>
For the first three alkanes, Hofmann used by then already established roots: </p>
<ul>
<li> ‘meth’, created in 1834 by <a href="http://en.wikipedia.org/wiki/Jean-Baptiste_Dumas" target="_blank" title="Jean-Baptiste Dumas in Wikipedia">Jean-Baptiste Dumas</a> and <a href="http://en.wikipedia.org/wiki/Eug%C3%A8ne-Melchior_P%C3%A9ligot" target="_blank" title="Eugène-Melchior Péligot in Wikipedia">Eugène Péligot</a> from the Greek <a href="http://en.wiktionary.org/wiki/%CE%BC%CE%AD%CE%B8%CF%85#Ancient_Greek" target="_blank" title="μέθυ in Wiktionary">μέθυ</a> (<i>méthu</i>, “wine”) and <a href="http://en.wiktionary.org/wiki/%E1%BD%95%CE%BB%CE%B7#Ancient_Greek" target="_blank" title="ὕλη in Wiktionary">ὕλη</a> (<i>húlē</i>, “wood”) to give a more scientificky name to <a href="http://en.wikipedia.org/wiki/Methanol" target="_blank" title="Methanol in Wikipedia">wood alcohol</a> (i.e. methanol) [3]. In his <a href="http://chem125-oyc.webspace.yale.edu/125/history99/5Valence/Nomenclature/Hofmannaeiou.html" target="_blank" title="Hofmann's Proposal for Systematic Nomenclature of the Hydrocarbons “On the Action of Trichloride of Phosphorus on the Salts of the Aromatic Monamines” by A. W. Hofmann, LL.D., F.R.S., &c.- Footnote on pp. 57-58">footnote</a> Hoffman equates the word <a href="http://en.wiktionary.org/wiki/methyl" target="_blank" title="methyl in Wiktionary">methyl</a> with the group CH<sub>3</sub>. </li>
<li> ‘eth’, from <a href="http://en.wikipedia.org/wiki/Ether" target="_blank" title="Ether in Wikipedia">ether</a> and that ultimately from Greek <a href="http://en.wiktionary.org/wiki/%CE%B1%E1%BC%B0%CE%B8%CE%AE%CF%81#Ancient_Greek" target="_blank" title="αἰθήρ in Wiktionary">αἰθήρ</a>. The name ‘æther’ was given to <a href="http://en.wikipedia.org/wiki/Diethyl_ether" target="_blank" title="Diethyl ether in Wikipedia">diethyl ether</a> C<sub>2</sub>H<sub>5</sub>–O–C<sub>2</sub>H<sub>5</sub> by <a href="http://en.wikipedia.org/wiki/August_Sigmund_Frobenius" target="_blank" title="August Sigmund Frobenius in Wikipedia">Joannes Sigismundus Augustus Frobenius</a> [4]. <a href="http://en.wikipedia.org/wiki/Justus_von_Liebig" target="_blank" title="Justus von Liebig in Wikipedia">Justus von Liebig</a> called the group C<sub>4</sub>H<sub>10</sub> <a href="http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/history/ether/ether.html" target="_blank" title="The Composition and Structure of Ether">‘ethyl radical’</a> [5] and gave it a symbol E; ‘æther’ was viewed as an oxide of ‘ethyl radical’. Hoffman, however, gives the word ‘ethyl’ its modern meaning, i.e. equates it with the group C<sub>2</sub>H<sub>5</sub>. </li>
<li> ‘prop’, from <a href="http://en.wikipedia.org/wiki/Propionic_acid" target="_blank" title="Propionic acid in Wikipedia">propionic acid</a>; the name <i>acide propionique</i> was proposed by Dumas <i>et al</i>. [6] from Greek <a href="http://en.wiktionary.org/wiki/%CF%80%CF%81%E1%BF%B6%CF%84%CE%BF%CF%82#Ancient_Greek" target="_blank" title="πρῶτος in Wiktionary">πρῶτος</a> (<i>prôtos</i>, “first”) and <a href="http://en.wiktionary.org/wiki/%CF%80%CE%AF%CF%89%CE%BD#Ancient_Greek" target="_blank" title="πίων in Wiktionary">πίων</a> (<i>píōn</i>, “fat”), because it is the first in the series of (true) fatty acids. Hoffman uses the word ‘propyl’ for the group C<sub>3</sub>H<sub>7</sub>.</li></ul>
<p> ‘Quartane’ did not catch on. Apparently, the root ‘but’, from <a href="http://en.wiktionary.org/wiki/butyl" target="_blank" title="butyl in Wiktionary">butyl</a> and that from <a href="http://en.wikipedia.org/wiki/Butyric_acid" target="_blank" title="Butyric acid in Wikipedia">butyric acid</a>, sounded better — or shall I say, butter? The name <i>acid butérique</i>, from Greek <a href="http://en.wiktionary.org/wiki/%CE%B2%CE%BF%CF%8D%CF%84%CF%85%CF%81%CE%BF%CF%82#Ancient_Greek" target="_blank" title="βούτυρος in Wiktionary">βούτυρος</a> (<i>boúturos</i>, “butter”), was coined in 1817 by <a href="http://en.wikipedia.org/wiki/Michel_Eug%C3%A8ne_Chevreul" target="_blank" title="Michel Eugène Chevreul in Wikipedia">Michel Eugène Chevreul</a> [7] who first isolated this “<i>principe odorant extrêmement remarquable</i>” from butter<sup>*</sup>. </p>
<p> Quintane, sextane, septane did not fare much better: Hofmann’s Latin multipliers had been replaced by Greek ones. Nevertheless, the principle of systematic naming outlined in that footnote, viz. multiplier + ‘ane’, has stayed. </p>
<center><p><a href="http://chemtymology.co.uk/2019/06/03/acetylene-and-hydrocarbon-suffixes/" target="_blank" title="Acetylene (and hydrocarbon suffixes) @ Chemtymology"><img border="0" src="http://chemtymology.files.wordpress.com/2019/06/hofmanns-scheme.png" /></a></p></center>
<p> Which brings us to the second point of Hoffman’s proposal: to use the series of vowels “a, e, i, o, u” to indicate the degree of saturation<sup>†</sup>. Somewhat confusingly for a present-day reader, Hoffman refers to anything beyond ‘ane’ as a “group”, so ‘yl’ corresponds to <i>univalent</i> group, ‘ene’ to <i>bivalent</i> group, ‘enyl’ to <i>trivalent</i> group, ‘ine’ to <i>quadrivalent</i> group, ‘inyl’ to <i>quintivalent</i> group and so on — as you can see, he was consistent in his use of Latin multipliers. It works fine with methane CH<sub>4</sub>: –CH<sub>3</sub> is methyl, –CH<sub>2</sub>– is ‘methene’ (now <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:50728" target="_blank" title="methylene group (CHEBI:50728)">methylene</a> or methanediyl) and –CH< is ‘methenyl’ (now <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29433" target="_blank" title="methanetriyl group (CHEBI:29433)">methanetriyl</a>). I wonder why there was no ‘methine’ for >CH< (now <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30039" target="_blank" title="methanetetrayl group (CHEBI:30039)">methanetetrayl</a>). In case of <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:42266" target="_blank" title="ethane (CHEBI:42266)">ethane</a>, Hoffman’s <i>terminology</i> stayed practically intact except that ‘ethine’ is called now ‘<a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27518" target="_blank" title="acetylene (CHEBI:27518)">ethyne</a>’ (all ‘i’s became ‘y’s in English). However, <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18153" target="_blank" title="ethene (CHEBI:18153)">ethene</a> or ethyne in modern sense are not groups but molecules, and both <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37603" target="_blank" title="vinyl group (CHEBI:37603)">ethenyl</a> and ethynyl are univalent groups. Likewise, <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32879" target="_blank" title="propane (CHEBI:32879)">propane</a>, <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16052" target="_blank" title="propene (CHEBI:16052)">propene</a> and <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:48086" target="_blank" title="propyne (CHEBI:48086)">propyne</a> are molecules and propanyl, propenyl and propynyl are univalent groups. </p>
<p> Note that in Hoffman’s proposal alkyl groups already have lost the ‘an’ bit: methane → methyl (not <strike>methanyl</strike>), ethane → ethyl (not <strike>ethanyl</strike>), propane → propyl (not <strike>propanyl</strike>) and so on, while the ‘en’ and ‘in’ (as well as ‘on’ and ‘un’) bits are conserved: ethene → ethenyl, ethine → ethinyl, propene → propenyl, propine → propinyl, etc. </p>
<p> Today we identify ‘en’ with double bond and ‘yn’ with triple bond. As there are no known quadruple or quintuple bonds between main-group atoms, there seems to be little use for ‘on’ and ‘un’ in Hoffman’s sense. But if they do exist? The <a href="http://metallome.blogspot.com/2012/02/carbon-carbon-quadruple-bond.html" target="_blank" title="Carbon—carbon quadruple bond @ this blog">2012 study</a> proposing the quadruple bond in <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30083" target="_blank" title="dicarbon (CHEBI:30083)">dicarbon</a> has stirred up much controversy. Even so, the recent discovery of boron–metal quadruple bonds [8, 9] makes me hopeful that “carbon and first-row main elements are open to quadruple bonding” [10]. Well, ‘one’ is out of question as it is used in ketones. But I think we still can employ ‘un’. Could we call C≣C ‘ethune’? </p>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> Trivial names such as German <a href="http://de.wikipedia.org/wiki/Butters%C3%A4ure" target="_blank" title="Buttersäure in German Wikipedia"><i>Buttersäure</i></a>, Swedish <a href="http://sv.wikipedia.org/wiki/Sm%C3%B6rsyra" target="_blank" title="Smörsyra in Swedish Wikipedia"><i>smörsyra</i></a> and Russian <a href="http://ru.wikipedia.org/wiki/%D0%9C%D0%B0%D1%81%D0%BB%D1%8F%D0%BD%D0%B0%D1%8F_%D0%BA%D0%B8%D1%81%D0%BB%D0%BE%D1%82%D0%B0" target="_blank" title="Масляная кислота в Википедии">масляная кислота</a> all mean “butter acid”. </td>
</tr>
<tr><td valign="top">†</td>
<td> From phonology point of view, “u, o, a, e, i” would be more logical. </td></tr>
</table>
<h4> References </h4>
<ol>
<li> Hofmann, A.W. (1866) On the action of trichloride of phosphorus on the salts of the aromatic monamines. <a href="http://royalsocietypublishing.org/doi/pdf/10.1098/rspl.1866.0018" target="_blank" title="Hofmann (1866) Proc. R. Soc. London 15, 54-62"><i>Proceedings of the Royal Society of London</i> <b>XV</b>, 54—62</a>. </li>
<li> Dixon, J. Acetylene (and hydrocarbon suffixes). <a href="http://chemtymology.co.uk/2019/06/03/acetylene-and-hydrocarbon-suffixes/" target="_blank" title="Acetylene (and hydrocarbon suffixes) @ Chemtymology"><i>Chemtymology</i>, 3 June 2019</a>. </li>
<li> Wisniak, J. (2009) Eugène Melchior Peligot. <a href="http://doi.org/10.1016/S0187-893X(18)30008-9" target="_blank" title="Wisniak, J. (2009) Educación Química 20, 61-69."><i>Educación Química</i> <b>20</b>, 61—69</a>.</li>
<li> Frobenius, J.S.A. (1730) An account of a spiritus vini æthereus, together with several experiments tried therewith. <a href="http://doi.org/10.1098/rstl.1729.0045" target="blank" title="Frobenius (1730) Phil. Trans. R. Soc. London 36, 283–289."><i>Philosophical Transactions of the Royal Society of London</i> <b>36</b>, 283—289</a>. </li>
<li> Ziegler, F.E. <a href="http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/history/ether/ether.html" target="_blank" title="The Composition and Structure of Ether">The Composition and Structure of Ether</a>. </li>
<li> Dumas, J.-B., Malaguti, F. and Leblanc, F. (1847) Sur l’identité des acides métacétonique et butyro-acétique. <a href="http://gallica.bnf.fr/ark:/12148/bpt6k2982c/f785" target="_blank" title="Dumas et al. (1847) Comptes Rendus 25, 781-784."><i>Comptes rendus hebdomadaires des séances de l’Académie des sciences</i> <b>XXV</b>, 781—784</a>.</li>
<li> McBride, J.M. <a href="http://chem125-oyc.webspace.yale.edu/125/history99/5Valence/Nomenclature/alkanenames.html" target="_blank" title="Development of Systematic Names for the Simple Alkanes by J.M.McBride">Development of systematic names for the simple alkanes</a>. </li>
<li> Chi, C., Wang, J.-Q., Hu, H.-S., Zhang, Y.-Y., Li, W.-L., Meng, L., Luo, M., Zhou, M. and Jun Li, J. (2019) Quadruple bonding between iron and boron in the BFe(CO)<sub>3</sub><sup>−</sup> complex. <a href="http://doi.org/10.1038/s41467-019-12767-5" target="_blank" title="Chi et al. (2019) Nat. Commun. 10, 4713."><i>Nature Communications</i> <b>10</b>, 4713</a>. </li>
<li> Cheung, L.F., Chen, T.-T., Kocheril, G.S., Chen, W.-J., Czekner, J. and Wang, L.-S. (2020) Observation of four-fold boron–metal bonds in RhB(BO<sup>–</sup>) and RhB. <a href="http://doi.org/10.1021/acs.jpclett.9b03484" target="_blank" title="Cheung et al. (2020) J. Phys. Chem. Lett. 11, 659-663."><i>The Journal of Physical Chemistry Letters</i> <b>11</b>, 659—663</a>. </li>
<li> Shaik, S., Danovich, D., Braida, B and Hiberty, P.C. (2016) The quadruple bonding in C<sub>2</sub> reproduces the properties of the molecule. <a href="http://doi.org/10.1002/chem.201600011" target="_blank" title="Shaik et al. (2016) Chem. Eur. J. 22, 4116-4128"><i>Chemistry – A European Journal</i> <b>22</b>, 4116—4128</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-42466318203636267682021-02-01T23:00:00.009+00:002024-02-26T17:12:00.632+00:00Carbon chains<p> Introduction aside, almost every organic chemistry textbook begins with <a href="http://goldbook.iupac.org/terms/view/A00222" target="_blank" title="alkanes in Gold Book">alkanes</a>, that is, acyclic <a href="http://goldbook.iupac.org/terms/view/H02889" target="_blank" title="hydrocarbons in Gold Book">hydrocarbons</a> with the general formula C<sub><i>n</i></sub>H<sub>2<i>n</i>+2</sub>. Maybe because of that, chemists tend to think of their naming as something too basic and thus boring. I myself thought so until coming across the book by Edward Godly [1] who, in a stroke of genius, put the chapter on silicon chains [1, pp. 19—21] <i>before</i> the chapter on hydrocarbon chains [1, pp. 25—28]. It prompted me to compare the naming of the two classes side-by-side. </p>
<a name='more'></a>
<p> Let’s start with unbranched alkanes, also known as linear alkanes, straight-chain alkanes, or <i>n</i>-alkanes (<i>n</i> for “normal”). Now that we know <a href="http://metallome.blogspot.com/2021/01/chains-and-rings.html" target="_blank" title="Chains and rings @ this blog">what chains are</a>, we can see that, from propane up, <i>n</i>-alkanes can be defined as saturated carbon chains. (According to our definition, methane and ethane are <i>not</i> chains, carbon or otherwise.) Univalent groups derived from alkanes are called <a href="http://goldbook.iupac.org/terms/view/A00228" target="_blank" title="alkyl groups in Gold Book">alkyl groups</a>, and alkyl groups derived by removal of a hydrogen atom from a <i>terminal</i> carbon atom of <i>n</i>-alkanes are called, somewhat unsurprisingly, <i>n</i>-alkyl groups. I put the names of <i>n</i>-alkanes, corresponding <i>n</i>-alkyl groups and their silicon analogues in the table below. </p>
<center>
<table>
<tr><th>Order</th> <th align="left">Formula</th> <th align="left">Name</th> <th align="left">Group</th> <th align="left">Name</th> <th align="left">Formula</th> <th align="left">Name</th> <th align="left">Group</th> <th align="left">Name</th> </tr>
<tr><th>1</th> <td>CH<sub>4</sub></td> <td>methane</td> <td>–CH<sub>3</sub></td> <td>methyl</td> <td>SiH<sub>4</sub></td> <td>silane</td><td>–SiH<sub>3</sub></td> <td>silyl</td> </tr>
<tr><th>2</th> <td>H<sub>3</sub>C–CH<sub>3</sub></td> <td>ethane</td> <td>–CH<sub>2</sub>–CH<sub>3</sub></td> <td>ethyl</td> <td>H<sub>3</sub>Si–SiH<sub>3</sub></td> <td>disilane</td> <td>–SiH<sub>2</sub>–SiH<sub>3</sub></td> <td>disilanyl</td> </tr>
<tr><th>3</th> <td>H<sub>3</sub>C–CH<sub>2</sub>–CH<sub>3</sub></td> <td>propane</td> <td>–[CH<sub>2</sub>]<sub>2</sub>–CH<sub>3</sub></td> <td>propyl</td> <td>H<sub>3</sub>Si–SiH<sub>2</sub>–SiH<sub>3</sub></td> <td>trisilane</td> <td>–[SiH<sub>2</sub>]<sub>2</sub>–SiH<sub>3</sub></td> <td>trisilanyl</td></tr>
<tr><th>4</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>2</sub>–CH<sub>3</sub></td> <td>butane</td> <td>–[CH<sub>2</sub>]<sub>3</sub>–CH<sub>3</sub></td> <td>butyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>2</sub>–SiH<sub>3</sub></td> <td>tetrasilane</td> <td>–[SiH<sub>2</sub>]<sub>3</sub>–SiH<sub>3</sub></td> <td>tetrasilanyl</td></tr>
<tr><th>5</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>3</sub>–CH<sub>3</sub></td> <td>pentane</td> <td>–[CH<sub>2</sub>]<sub>4</sub>–CH<sub>3</sub></td> <td>pentyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>3</sub>–SiH<sub>3</sub></td> <td>pentasilane</td> <td>–[SiH<sub>2</sub>]<sub>4</sub>–SiH<sub>3</sub></td> <td>pentasilanyl</td></tr>
<tr><th>6</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>4</sub>–CH<sub>3</sub></td> <td>hexane</td> <td>–[CH<sub>2</sub>]<sub>5</sub>–CH<sub>3</sub></td> <td>hexyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>4</sub>–SiH<sub>3</sub></td> <td>hexasilane</td> <td>–[SiH<sub>2</sub>]<sub>5</sub>–SiH<sub>3</sub></td> <td>hexasilanyl</td></tr>
<tr><th>7</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>5</sub>–CH<sub>3</sub></td> <td>heptane</td> <td>–[CH<sub>2</sub>]<sub>6</sub>–CH<sub>3</sub></td> <td>heptyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>5</sub>–SiH<sub>3</sub></td> <td>heptasilane</td> <td>–[SiH<sub>2</sub>]<sub>6</sub>–SiH<sub>3</sub></td> <td>heptasilanyl</td></tr>
<tr><th>8</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>6</sub>–CH<sub>3</sub></td> <td>octane</td> <td>–[CH<sub>2</sub>]<sub>7</sub>–CH<sub>3</sub></td> <td>octyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>6</sub>–SiH<sub>3</sub></td> <td>octasilane</td> <td>–[SiH<sub>2</sub>]<sub>7</sub>–SiH<sub>3</sub></td> <td>octasilanyl</td></tr>
<tr><th>9</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>7</sub>–CH<sub>3</sub></td> <td>nonane</td> <td>–[CH<sub>2</sub>]<sub>8</sub>–CH<sub>3</sub></td> <td>nonyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>7</sub>–SiH<sub>3</sub></td> <td>nonasilane</td> <td>–[SiH<sub>2</sub>]<sub>8</sub>–SiH<sub>3</sub></td> <td>nonasilanyl</td></tr>
<tr><th>10</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>8</sub>–CH<sub>3</sub></td> <td>decane</td> <td>–[CH<sub>2</sub>]<sub>9</sub>–CH<sub>3</sub></td> <td>decyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>8</sub>–SiH<sub>3</sub></td> <td>decasilane</td> <td>–[SiH<sub>2</sub>]<sub>9</sub>–SiH<sub>3</sub></td> <td>decasilanyl</td></tr>
<tr><th>11</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>9</sub>–CH<sub>3</sub></td> <td>undecane</td> <td>–[CH<sub>2</sub>]<sub>10</sub>–CH<sub>3</sub></td> <td>undecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>9</sub>–SiH<sub>3</sub></td> <td>undecasilane</td> <td>–[SiH<sub>2</sub>]<sub>10</sub>–SiH<sub>3</sub></td> <td>undecasilanyl</td></tr>
<tr><th>12</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>10</sub>–CH<sub>3</sub></td> <td>dodecane</td> <td>–[CH<sub>2</sub>]<sub>11</sub>–CH<sub>3</sub></td> <td>dodecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>10</sub>–SiH<sub>3</sub></td> <td>dodecasilane</td> <td>–[SiH<sub>2</sub>]<sub>11</sub>–SiH<sub>3</sub></td> <td>dodecasilanyl</td></tr>
<tr><th>13</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>11</sub>–CH<sub>3</sub></td> <td>tridecane</td> <td>–[CH<sub>2</sub>]<sub>12</sub>–CH<sub>3</sub></td> <td>tridecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>11</sub>–SiH<sub>3</sub></td> <td>tridecasilane</td> <td>–[SiH<sub>2</sub>]<sub>12</sub>–SiH<sub>3</sub></td> <td>tridecasilanyl</td></tr>
<tr><th>14</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>12</sub>–CH<sub>3</sub></td> <td>tetradecane</td> <td>–[CH<sub>2</sub>]<sub>13</sub>–CH<sub>3</sub></td> <td>tetradecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>12</sub>–SiH<sub>3</sub></td> <td>tetradecasilane</td> <td>–[SiH<sub>2</sub>]<sub>13</sub>–SiH<sub>3</sub></td> <td>tetradecasilanyl</td></tr>
<tr><th>15</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>13</sub>–CH<sub>3</sub></td> <td>pentadecane</td> <td>–[CH<sub>2</sub>]<sub>14</sub>–CH<sub>3</sub></td> <td>pentadecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>13</sub>–SiH<sub>3</sub></td> <td>pentadecasilane</td> <td>–[SiH<sub>2</sub>]<sub>14</sub>–SiH<sub>3</sub></td> <td>pentadecasilanyl</td></tr>
<tr><th>16</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>14</sub>–CH<sub>3</sub></td> <td>hexadecane</td> <td>–[CH<sub>2</sub>]<sub>15</sub>–CH<sub>3</sub></td> <td>hexadecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>14</sub>–SiH<sub>3</sub></td> <td>hexadecasilane</td> <td>–[SiH<sub>2</sub>]<sub>15</sub>–SiH<sub>3</sub></td> <td>hexadecasilanyl</td></tr>
<tr><th>17</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>15</sub>–CH<sub>3</sub></td> <td>heptadecane</td> <td>–[CH<sub>2</sub>]<sub>16</sub>–CH<sub>3</sub></td> <td>heptadecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>15</sub>–SiH<sub>3</sub></td> <td>heptadecasilane</td> <td>–[SiH<sub>2</sub>]<sub>16</sub>–SiH<sub>3</sub></td> <td>heptadecasilanyl</td></tr>
<tr><th>18</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>16</sub>–CH<sub>3</sub></td> <td>octadecane</td> <td>–[CH<sub>2</sub>]<sub>17</sub>–CH<sub>3</sub></td> <td>octadecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>16</sub>–SiH<sub>3</sub></td> <td>octadecasilane</td> <td>–[SiH<sub>2</sub>]<sub>17</sub>–SiH<sub>3</sub></td> <td>octadecasilanyl</td></tr>
<tr><th>19</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>17</sub>–CH<sub>3</sub></td> <td>nonadecane</td> <td>–[CH<sub>2</sub>]<sub>18</sub>–CH<sub>3</sub></td> <td>nonadecyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>17</sub>–SiH<sub>3</sub></td> <td>nonadecasilane</td> <td>–[SiH<sub>2</sub>]<sub>18</sub>–SiH<sub>3</sub></td> <td>nonadecasilanyl</td></tr>
<tr><th>20</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>18</sub>–CH<sub>3</sub></td> <td>icosane</td> <td>–[CH<sub>2</sub>]<sub>19</sub>–CH<sub>3</sub></td> <td>icosyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>18</sub>–SiH<sub>3</sub></td> <td>icosasilane</td> <td>–[SiH<sub>2</sub>]<sub>19</sub>–SiH<sub>3</sub></td> <td>icosasilanyl</td></tr>
<tr><th>21</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>19</sub>–CH<sub>3</sub></td> <td>henicosane</td> <td>–[CH<sub>2</sub>]<sub>20</sub>–CH<sub>3</sub></td> <td>henicosyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>19</sub>–SiH<sub>3</sub></td> <td>henicosasilane</td> <td>–[SiH<sub>2</sub>]<sub>20</sub>–SiH<sub>3</sub></td> <td>henicosasilanyl</td></tr>
<tr><th>22</th> <td>H<sub>3</sub>C–[CH<sub>2</sub>]<sub>20</sub>–CH<sub>3</sub></td> <td>docosane</td> <td>–[CH<sub>2</sub>]<sub>21</sub>–CH<sub>3</sub></td> <td>docosyl</td> <td>H<sub>3</sub>Si–[SiH<sub>2</sub>]<sub>20</sub>–SiH<sub>3</sub></td> <td>docosasilane</td> <td>–[SiH<sub>2</sub>]<sub>21</sub>–SiH<sub>3</sub></td> <td>docosasilanyl</td></tr>
</table>
</center>
<p> And so on and so forth, you get the picture. Apart from the <a href="http://metallome.blogspot.com/2021/02/hofmanns-footnote.html" target="_blank" title="von Hofmann’s footnote @ this blog">first four hydrocarbons</a>, the rest appears to be named in a pretty regular fashion: a name consists of a <a href="http://metallome.blogspot.com/2020/10/prefixes-or-combining-forms.html" target="_blank" title="Prefixes — or combining forms? @ this blog">multiplier</a> corresponding to the number of carbon atoms in a chain followed by ‘ane’. If you don’t look at the right part of the table, that is. </p>
<p> First you might have noticed the absence of “carbon” from the hydrocarbon names. By comparison, silicon hydrides all have the combining form ‘sil’ (which is a truncated form of the root ‘silic’) in them. Thus, the name ‘hexasilane’ can be easily analysed in terms of combining forms ‘hex(a)’ = six, ‘sil’ = silicon and ‘an’ = hydride, i.e. “hydride containing six silicon atoms”. On the other hand, ‘hexane’ means just “hydride containing six non-hydrogen atoms”. This sounds natural to organic chemists because for them carbon is a default element and saying ‘hexacarbane’ is too much a bother. </p>
<p> Next, note that <i>n</i>-alkyl group names, just like the word ‘alkyl’ (not <strike>alkanyl</strike>), all uniformly lack the ‘an’ bit: methane → methyl (not <strike>methanyl</strike>), ethane → ethyl (not <strike>ethanyl</strike>), decane → decyl (not <strike>decanyl</strike>)... In contrast, their silicon counterparts keep ‘an’ as in <i>x</i>-silane → <i>x</i>-silanyl, with the singular exception of <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30541" target="_blank" title="silyl group (CHEBI:30541)">silyl</a> group<sup>*</sup>. </p>
<p> Not all alkyl group names lose ‘an’ though. Starting with propane, there is more than one way to form a group. So if the <i>n</i>-alkyl group –CH<sub>2</sub>–CH<sub>3</sub> is called ‘<a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:26308" target="_blank" title="propyl group (CHEBI:26308)">propyl</a>’ (no need to name it ‘propan-1-yl’), the group ‒CH(CH<sub>3</sub>)<sub>2</sub> derived from propane by removal of a hydrogen from the carbon-2 atom is named systematically ‘propan-2-yl’ (acceptable alternative name ‘<a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30353" target="_blank" title="isopropyl group (CHEBI:30353)">isopropyl</a>’). </p>
<p> Let us now move on to <a href="http://goldbook.iupac.org/terms/view/A00224" target="_blank" title="alkenes in Gold Book">alkenes</a> and <a href="http://goldbook.iupac.org/terms/view/A00236" target="_blank" title="alkynes in Gold Book">alkynes</a>. Their names are derived from the names of corresponding alkanes by replacing the ‘an’ with ‘en’ for a double carbon–carbon bond and with ‘yn’ for a triple carbon–carbon bond. In my humble opinion, the resulting names are <i>not</i> <a href="http://goldbook.iupac.org/terms/view/S06085" target="_blank" title="subtractive name in Gold Book">subtractive</a> in spite of some publications, including the IUPAC guides, referring to ‘ene’ and ‘yne’ as “<a href="http://metallome.blogspot.com/2020/12/suffixes-or-combining-forms.html" target="_blank" title="Suffixes — or combining forms? @ this blog">subtractive suffixes</a>”. We can also think of ‘an’ → ‘en’ operation as a <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">substitution</a> of two implicit hydrogen atoms with one <a href="http://en.wikipedia.org/wiki/Pi_bond" target="_blank" title="Pi bond in Wikipedia">π-bond</a> as if this bond were a divalent substituent –π–, and similarly ‘an’ → ‘yn’ as a substitution of four implicit hydrogens with two π-bonds as if they were a tetravalent substituent =π=. Yet these operations do not create your typical substitutive names either. I believe the ‘en’ and ‘yn’ operations are truly in a class of their own. The linguistic analogue is a vowel mutation like <a href="http://en.wikipedia.org/wiki/Germanic_umlaut" target="_blank" title="Germanic umlaut in Wikipedia">umlaut</a> (Modern English examples include <i>fall</i>/<i>fell</i>, <i>foot</i>/<i>feet</i> and <i>man</i>/<i>men</i>). I have to think more about this. </p>
<p> In chains longer than three carbons, the positions of unsaturated bonds should be indicated by locants immediately preceding the ‘en’ or ‘yn’. Only <i>one</i>, the lower, locant is cited for each pair. Compare that with genuine <a href="http://metallome.blogspot.com/2020/07/subtractive-names.html" target="_blank" title="Subtractive names @ this blog">subtractive names</a> where ‘didehydro’, ‘tetradehydro’, etc. are always preceded by <i>pairs</i> of locants indicating the positions of atoms that lose hydrogens, as in ‘1,2-didehydro’. </p>
<p> Since we need at least one carbon–carbon bond to start with, the simplest unsaturated hydrocarbons can be derived from ethane <b>(a)</b>. Accordingly, the structure <b>(b)</b> is systematically named ethene and <b>(c)</b> ethyne. So far so good. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:42266" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="ethane (CHEBI:42266)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhE-35Zm7z_KnOh_ss_XXG-L8MQJ5c883uIPSX8jFdgVrqRfxEZg7ceHqkPSw3VzlMao7Dhsz7XmJ6uhAAajQJKGxrPiH7G6GfhLKQ4CR3RzvLPl1ltdPnQJe6Zv0THQe8PJkdVcg/s0/ethane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:18153" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="ethene (CHEBI:18153)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNha31oq5sdruZNP0l8mnwTuiM5KQAMNlCKcv-N1p4a6ElkmyZf9Ce-56rY42Q5eGpXY_K6WI3TXqhomPI2r6P-soT2DpOskeeIIb3NleTQlQ5_0r6uPWQ9c_t5qGRp8yRJhZwKw/s0/ethene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27518" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="acetylene (CHEBI:27518)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_BZnAhGb3aLDR7aj4he1PEBwpJr9VMuYH5B9ZaSB6vZsld9GgLj-XTdb1DrO3mkDouVXZsUzOfJGrK3YVjPbdUfwx4bFXu-BgEQo95s6alMQKjePDqypb6vRjNQ9cMGcZacBaCw/s0/acetylene.png" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th> <th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> H<sub>3</sub>C–CH<sub>3</sub> <br />
ethane </li>
<li> H<sub>2</sub>C=CH<sub>2</sub> <br />
ethene <br />
ethylene (<i>trivial</i>) </li>
<li> HC≡CH <br />
ethyne <br />
acetylene (<i>trivial</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> The next in the series is propane <b>(d)</b>. Replacing one of its C–C bonds with C=C results in the structure <b>(e)</b> called prop-1-ene or, shorter, propene<sup>†</sup>. Makes sense? </p>
<p> It kind of does. But what about the second carbon–carbon bond which stays single? Shouldn’t the modified structure be named prop-1-en-2-ane (or prop-1-an-2-ene)? This, however, would result in much longer names. </p>
<p> Likewise, replacing one of C–C bonds in <b>(d)</b> with C≡C we get <b>(f)</b> called prop-1-yne, or simply propyne<sup>†</sup>. So the systematic names of alkenes and alkynes <i>imply</i> that all carbon–carbon bonds are single unless otherwise stated — another disappearing act of ‘an’. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:32879" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="propane (CHEBI:32879)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFsJf6g4JSycVGdrYWd2ON_cc0ngzH3D4tYnnQehq-ZpwTrH4MbvajMj2Ka-jlcw0cv_gZkFkCFy5JbHD_CcgHVX_ya1E1i8_XZMMaHhU125aR2ixLy1Dod8MJgrvrs6DgutsJoA/s0/propane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16052" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="propene (CHEBI:16052)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_-5GNQteG_35ZsSn2IqccHw8RSnJy2Ja0TeIjEbXTW9JL4EU1qfhSMh615SMr1x63lFIE4dRVClvgUYnaI9_SbNNku059trT5ThgplRhthMtEToG7dPAzSN-i17vFF_cJ4MMtbQ/s0/propene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:48086" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="propyne (CHEBI:48086)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh4HFyMxovG6jrSzi_iPxtHs7eCY02VKPmdjD9lQfOvFsVphzj3W9LlysoQYSDoZNOro6LfNqIZJOBLt7wygBVzhF1LSKci0DvAG_1k-SYk5ts1LX1W5we5iCOlBw1mwfBQZlyMIw/s0/propyne.png" /></a></td>
</tr>
<tr><th align="center">(d)</th> <th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="4" type="a">
<li> H<sub>3</sub>C–CH<sub>2</sub>–CH<sub>3</sub> <br />
propane </li>
<li> H<sub>2</sub>C=CH–CH<sub>3</sub> <br />
propene <br />
prop-1-ene </li>
<li> HC≡C–CH<sub>3</sub> <br />
propyne <br />
prop-1-yne </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Consider undecane <b>(g)</b> that has ten carbon–carbon bonds. In case of undec-1-ene <b>(h)</b>, only one carbon–carbon bond is double; the remaining bonds are still single. I think it is a bit unfair to call undec-1-ene alkene when it is 90% alkane; ditto undec-1-yne <b>(i)</b>. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:46342" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="undecane (CHEBI:46342)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2-LWv3kVsX0WbZ88TZPQ9ee71wEbCvGFiYYAnZPuXnZNx2m3EOj10JjRvjea-6CISPgDpc4RtDNos0v7FQfxu63-fzIYZEReZPRnRdRUlwUXbvnsgNIzdOP47kYeGQ0MywjH2dg/s0/undecane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:77444" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1-undecene (CHEBI:77444)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi3PymDwc-6RdaQY6nPnK4QLuFwpYZFhdoCX1sXYoQ4THZmF1aOW8vLnvT13jxAsMkEV5Fjh7ekm3Xqtp6PWX5uSEZ4Qchk37YtoVH9Sv5u5IFPsuuR8dJW5NWXxtFwgRA6XDcUpA/s0/1-undecene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:87545" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="1-undecyne (CHEBI:87545)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgokjtkB-nupKPHpGMKOCzjukj6ruMfrGJW11a8f71lPC5Kts9DJJTrPi8HlUA7iIHNhIFoFGGj-v7zWn8Qe306vMcHqYNN8N-hbOelY1tt7gZ-CrSk7EBkwRHS5MEmKMku1PKyjA/s0/1-undecyne.png" /></a></td>
</tr>
<tr><th align="center">(g)</th> <th align="center">(h)</th> <th align="center">(i)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="7" type="a">
<li> H<sub>3</sub>C–[CH<sub>2</sub>]<sub>9</sub>–CH<sub>3</sub> <br />
undecane</li>
<li> H<sub>2</sub>C=CH–[CH<sub>2</sub>]<sub>8</sub>–CH<sub>3</sub> <br />
undec-1-ene </li>
<li> HC≡C–[CH<sub>2</sub>]<sub>8</sub>–CH<sub>3</sub> <br />
undec-1-yne </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Here’s a summary of groups derived from structures <b>(a)</b>—<b>(f)</b>: </p>
<center>
<table cellpadding="10">
<tr> <th align="left">Alkane</th> <th align="left">Alkyl group</th> <th align="left">Alkene</th> <th align="left">Alkenyl group</th> <th align="left">Alkyne</th> <th>Alkynyl group</th> </tr>
<tr> <td>H<sub>3</sub>C–CH<sub>3</sub> <br /> ethane</td> <td>–CH<sub>2</sub>–CH<sub>3</sub><br /> ethyl </td> <td>H<sub>2</sub>C=CH<sub>2</sub> <br /> ethene </td> <td>–CH=CH<sub>2</sub> <br /> ethenyl <br /> vinyl<sup>‡</sup> </td> <td>HC≡CH <br /> acetylene <br /> ethyne </td> <td>–C≡CH <br /> ethynyl</td></tr>
<tr><td rowspan="6">H<sub>3</sub>C–CH<sub>2</sub>–CH<sub>3</sub> <br /> propane </td> <td rowspan="3">–CH<sub>2</sub>–CH<sub>3</sub> <br /> propyl</td> <td rowspan="6">H<sub>2</sub>C=CH–CH<sub>3</sub> <br /> prop-1-ene</td> <td rowspan="2">–CH=CH–CH<sub>3</sub> <br /> prop-1-en-1-yl</td> <td rowspan="6">HC≡C–CH<sub>3</sub> <br /> prop-1-yne</td> <td rowspan="3">–C≡C–CH<sub>3</sub> <br /> prop-1-yn-1-yl</td></tr>
<tr></tr>
<tr><td rowspan="2">–CH<sub>2</sub>–CH=CH<sub>2</sub> <br /> prop-2-en-1-yl <br /> allyl<sup>‡</sup> </td></tr>
<tr><td rowspan="3">‒CH(CH<sub>3</sub>)<sub>2</sub> <br /> propan-2-yl <br /> isopropyl<sup>‡</sup> </td> <td rowspan="3">–CH<sub>2</sub>–C≡CH <br /> prop-2-yn-1-yl</td></tr>
<tr><td rowspan="2">–C(CH<sub>3</sub>)=CH<sub>2</sub> <br /> prop-1-en-2-yl <br /> isopropenyl<sup>‡</sup></td></tr>
</table>
</center>
<p> From four-carbon chain up, there are more than one isomer of <i>n</i>-alkene and <i>n</i>-alkyne and even more alkenyl and alkynyl groups. </p>
<p> If a structure has more than one double or triple bond, the multipliers ‘di-’, ‘tri-’, etc. are employed. Corresponding acyclic hydrocarbons are known as alkadienes, alkatrienes, alkadiynes, alkatriynes, etc. Hydrocarbons containing both double and triple bonds are called <a href="http://en.wikipedia.org/wiki/Enyne" target="_blank" title="Enyne in Wikipedia">enynes</a>, dienynes, enediynes and so on.
</p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37609" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="butatriene (CHEBI:37609)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_ruZ5Pf2fZ7Df3BNAJmny9aYSeBxW3OoVoSGJz4xFVolrOJLPpT5IR8lUQx31EpVz87Ceb8Xdy8ZxL5B2aWZ7S4OhZcpzhHr7Pb7pb8nR9XNCuGilU8sriiKny6tGT0L3FKZ7uw/s0/butatriene.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37823" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="deca-1,9-diyne (CHEBI:37823)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjo_0kjmc3G2IQQY64CixcjthoUT6NJP7wj13EhGCmXKif2j4yUI6_GXFtWj2Z1SA18_7i3V8jl9rRtSL4koI2Tv_Bi9pQmFCAy-u96pBoJ31yZBnT3dBzVDh0VnbBs2JQLOpHtEQ/s0/deca-1%252C9-diyne.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:2501" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="Aethusin (CHEBI:2501)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjkYxcYnYqUBSS2RhNrpZL75PPWhN6GwX8MW_Np1xMi2rogw7VoPN_M8RUAlgntf78sGwFVxoqPbXpGjg142X_XTuVAZWC9Iei5yyXt40StZ7ImfrvY7RkUOVRgna_yZX8k7jd54g/s0/aethusin.png" /></a></td>
</tr>
<tr><th align="center">(j)</th> <th align="center">(k)</th> <th align="center">(l)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="10" type="a">
<li> H<sub>2</sub>C=C=C=CH<sub>2</sub> <br />
buta-1,2,3-triene <br />
butatriene</li>
<li> HC≡C–[CH<sub>2</sub>]<sub>6</sub>–C≡CH <br />
deca-1,9-diyne </li>
<li> H<sub>3</sub>C–C=C–C≡C–C≡C–CH=CH–CH=CH–CH<sub>2</sub>–CH<sub>3</sub> <br />
aethusin (<i>trivial</i>) <br />
(2<i>E</i>,8<i>E</i>,10<i>E</i>)-trideca-2,8,10-triene-4,6-diyne </li>
</ol>
</td>
</tr>
</table>
</center>
<p> To sum up: </p>
<ul>
<li> In the systematic names of hydrocarbons neither hydrogen nor carbon are explicitly named. </li>
<li> The names of <i>n</i>-alkanes with more than five carbon atoms consist of a multiplier followed by the combining form ‘an’ and ending ‘e’. </li>
<li> The names of <i>n</i>-alkyl groups lose the combining form ‘an’; other groups derived from <i>n</i>-alkanes keep it. </li>
<li> The names of hydrocarbons derived from alkanes by replacing at least one carbon–carbon bond with double or triple bond (alkenes, alkynes etc.) also lose the ‘an’ which is being replaced by ‘en’ or ‘yn’, respectively. </li>
<li> The positions of unsaturated bonds are indicated by locants immediately preceding the ‘en’ or ‘yn’. Only one (the lower) locant is cited for every unsaturated bond. </li>
</ul>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> According to <a href="http://www.acdlabs.com/iupac/nomenclature/93/r93_355.htm" target="_blank" title="silyl @ ACDLabs">IUPAC recommendations</a> [2], the form ‘silyl’ is preferred to ‘silanyl’ in order to distinguish between two or more silyl (–SiH<sub>3</sub>) groups, i.e. ‘disilyl’, ‘trisilyl’, ‘tetrasilyl’, etc. and one disilanyl, trisilanyl, tetrasilanyl, etc. group, without using the multipliers ‘bis-’, ‘tris-’, ‘tetrakis-’, etc. </td>
</tr>
<tr><td valign="top">†</td>
<td> Here, locant can be omitted since there are only two bonds in the structure so there is no difference between, say, prop-1-ene and prop-2-ene. This is not the case for longer unsaturated carbon chains and therefore it is necessary to use locants.</td></tr>
<tr><td valign="top">‡</td>
<td> Acceptable alternative (non-systematic) name. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<li> Godly, E.W. <a href="https://amzn.to/3r2CR0E" target="_blank" title="Naming Organic Compounds: A Systematic Instruction Manual @ Amazon.co.uk"><i>Naming Organic Compounds: A Systematic Instruction Manual</i></a>, 2<sup>nd</sup> Ed. Ellis Horwood, Hemel Hempstead, 1995. </li>
<li> Panico, R., Powell, W.H. and Richer, J.-C. <i>A Guide to IUPAC Nomenclature of Organic Compounds (Recommendations 1993)</i>. Blackwell Science, 1993. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-56147335971235482052021-01-23T20:00:00.059+00:002023-08-07T10:12:50.895+01:00Chains and rings<p> After hours spent looking in my books and searching the internet, I came to the conclusion that chemists talk about chains and rings without explaining what they mean. The only definition I found so far, viz. <a href="http://goldbook.iupac.org/terms/view/C00946" target="_blank" title="chain (in polymers) in Gold Book">that of Gold Book</a>, is specific for polymers and seems to be too complex to be used in general chemical nomenclature: </p>
<table width="90%">
<tr>
<td width="90%"><blockquote> The whole or part of a <a href="http://goldbook.iupac.org/terms/view/M03667" target="_blank" title="macromolecule (polymer molecule) in Gold Book">macromolecule</a>, an <a href="http://goldbook.iupac.org/terms/view/O04286" target="_blank" title="oligomer molecule in Gold Book">oligomer molecule</a> or a <a href="http://goldbook.iupac.org/terms/view/B00682" target="_blank" title="block in Gold Book">block</a>, comprising a linear or branched sequence of <a href="http://goldbook.iupac.org/terms/view/C01288" target="_blank" title="constitutional unit in Gold Book">constitutional units</a> between two boundary constitutional units, each of which may be either an <a href="http://goldbook.iupac.org/terms/view/E02092" target="_blank" title="end-group in Gold Book">end-group</a>, a <a href="http://goldbook.iupac.org/terms/view/B00728" target="_blank" title="branch point (in polymers) in Gold Book">branch point</a> or an otherwise-designated characteristic feature of the macromolecule. </blockquote> </td>
<td align="right" width="10%"><b>(1)</b></td>
</tr>
</table>
<p> On the other hand, general dictionary definitions of (chemical) chains are not precise enough. For example, <a href="http://www.collinsdictionary.com/dictionary/english/chain" target="_blank" title="chain in Collins English Dictionary">Collins English Dictionary</a> defines chain (<i>chemistry</i>) as </p>
<table width="90%">
<tr>
<td width="90%"><blockquote> two or more atoms or groups bonded together so that the configuration of the resulting molecule, ion, or radical resembles a chain. </blockquote> </td>
<td align="right" width="10%"><b>(2)</b></td>
</tr>
</table>
<p> whereas <a href="http://www.merriam-webster.com/dictionary/chain" target="_blank" title="chain in Merriam-Webster">Merriam-Webster</a> says that it is </p>
<table width="90%">
<tr>
<td width="90%"><blockquote> a number of atoms or chemical groups united like links in a chain. </blockquote> </td>
<td align="right" width="10%"><b>(3)</b></td>
</tr>
</table>
<p> So chain (<i>chemistry</i>) is like a chain. Is it? </p>
<a name='more'></a>
<p> Well, there <i>is</i> a class of macromolecules called <a href="http://en.wikipedia.org/wiki/Catenane" target="_blank" title="Catenane in Wikipedia"><i>catenanes</i></a> that consist of at least two interlocked <a href="http://en.wikipedia.org/wiki/Macrocycle" target="_blank" title="Macrocycle in Wikipedia">macrocycles</a> (i.e. rings!) and so are, indeed, <i>like</i> a real chain. </p>
<center><a href="http://goldbook.iupac.org/terms/view/C00904" target="_blank" title="catenanes in Gold Book"><img border="0" src="http://goldbook.iupac.org/img/inline/C00904.png" /></a></center>
<p> Maybe we don’t need definitions. “You know it when you see it”, as they say. Of course, this “it” refers to a graphical representation of the structure in question. It seems obvious that the structure <b>(a)</b> is a chain while <b>(b)</b> is indubitably a ring. But what about <b>(c)</b>? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29021" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="hexane (CHEBI:29021)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsF_s5CogGCtVEjdxkS7cuOvQhMfPOPXiGy8ZBuXPIwxvQSAOzWF-s0vC64ewujlChH2ALtSzOvINmBUzC4ip9oBEJJ_ih7trUc2-Tecsa42zgfeRwGEolt32pNkQ1v3DBl0gX8Q/s0/hexane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29005" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="cyclohexane (CHEBI:29005)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPJOhSxBcicwYwYWtSg1ubhGtS51UFB3_LHf2SQvZL1bpxIiBQ_5LqAAh4vaO9fzCbvs9-1NQHy6QWukJuEohRRNwJkw0oaE1UmDe0mqWyl4V_SRQK0MDGWyEb7AntAIWKU94U-g/s1600/cyclohexane.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36480" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="bisabolane (CHEBI:36480)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGSrA8nOVUwT9SY-EukCJF4PXMM7-M4WsVL3ayipRgM8sWWapnVCksEvz1ZrFHgZmNf2T3XMEUW1T00gP5W_4bQqeWN4F-EMdM35JRwH_jHaMR53FPDYLYrzOovfdpCEDxAJ_q6w/s0/bisabolane.png" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th> <th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> hexane </li>
<li> cyclohexane </li>
<li> bisabolane (<i>trivial</i>) <br />
1-(1,5-dimethylhexyl)-4-methylcyclohexane (<i>substitutive</i>) <br />
1-methyl-4-(6-methylheptan-2-yl)cyclohexane (<i>substitutive</i>)
</li>
</ol>
</td>
</tr>
</table>
</center>
<p> When we talk about chains and rings, do we refer to the molecular entities or parts thereof? The example <b>(c)</b> above seems to suggest the latter, viz. that <b>(c)</b> contains the chain <b>(a)</b> and the ring <b>(b)</b>. </p>
<p> What’s the minimum number of atoms in a structure to be considered a chain? In my opinion, three. (Also, three is the minimum number of atoms in a ring.) Consider this: a <a href="http://en.wikipedia.org/wiki/Chain" target="_blank" title="Chain in Wikipedia">real chain</a> consists of at least two connected links. One link is <i>not</i> a chain; neither are two loose links. Likewise, chain in chemical sense should contain at least two <i>adjacent</i> chemical bonds. One dioxygen molecule, O=O, is not a chain; two dioxygen molecules still are not a chain. The ozone molecule, O=O=O, <i>is</i> a chain. Is the structure <b>(d)</b> a chain then? </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16136" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="hydrogen sulfide (CHEBI:16136)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEid3BuirEtOuCZI1gHZmzqoLY1xDRztTTFyq1Dcxtg3jHhZhMlKUX84f7KGeYGqdLsYSOxu_wBylRTNeG6rj7wTBMDxMlrJZFNx5_z6NJtcaWxfzO8yMc5oOVyNETuDJgWVi-99Fg/s0/hydrogen_sulfide.png" /></a></td>
</tr>
<tr><th align="center">(d)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="4" type="a">
<li> H<sub>2</sub>S <br />
hydrogen sulfide (<i>binary</i>) <br />
dihydridosulfur (<i>additive</i>) <br />
sulfane (<i>parent hydride</i>) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> Why, H–S–H looks like a chain to me: three atoms, two adjacent bonds. But I already hear people protesting. Inorganic chemists are likely to think of SH<sub>2</sub> as a <a href="http://metallome.blogspot.com/2020/06/addictive-names.html" target="_blank" title="Addi(c)tive names @ this blog">mononuclear structure</a>, while for organic chemists it is a <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">parent hydride</a>; the hydrogens are not considered a part of a skeleton. Typical graphical representations of organic structures do not show any hydrogens bound to carbon atoms, except for terminal ones maybe. </p>
<p> Yet the hydrogens are there. So, the structure <b>(e)</b> <i>is</i> a chain and the structure <b>(f)</b> <i>is</i> a ring. </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30479" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="trihydrogen(1+) (CHEBI:30479)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLNpknjGlmyA7itixr38AtPppWI-AWGlDC5kUljKF6u-b4sfH8Sz9RlAxt1OML5FtFT_U4ExVyXUpgdKQ7LmATWu36F8u0YYewhIhppD2Xr8qDyCH3Ck31E-uB7-EeNlp4QaIkhw/w200-h200/trihydrogen%25281%252B%2529.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:33590" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="diborane(6) (CHEBI:33590)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjydZrknlOedc2UteSbTei84gSIk-oDxhDCEx2X_se3F-gBaLuclW7Jm-PfQig1JtKw2Tilqqb8jC263xOvajGuvGEsKmy4lF4RuDqWMtEkdAwTKAoyVvBioWvGeJ9Jt6zZUAMkCg/s0/diborane%25286%2529.png" /></a></td>
</tr>
<tr><th align="center">(e)</th> <th align="center">(f)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="5" type="a">
<li> H<sub>3</sub><sup>+</sup> <br /> trihydrogen(1+) </li>
<li> B<sub>2</sub>H<sub>6</sub> <br /> diborane(6) </li>
</ol>
</td>
</tr>
</table>
</center>
<p> If structural formula can tell us whether the molecular entity in question contains chain(s) or ring(s), it only seems logical to define chains and rings on the basis of structural formulae. It surely must have been done already by those working in <a href="http://topicpageswiki.plos.org/wiki/Chemical_Graph_Theory" target="_blank" title="Chemical graph theory @ PLOS Wiki">chemical graph theory</a>. I just can’t find those definitions spelled out in black and white. </p>
<p> Let’s think of a structural formula as a <a href="http://en.wikipedia.org/wiki/Graph_(discrete_mathematics)" target="_blank" title="Graph (discrete mathematics) in Wikipedia">graph</a> in a hope that we can take all what we need from <a href="http://en.wikipedia.org/wiki/Graph_theory" target="_blank" title="Graph theory in Wikipedia">graph theory</a>. So... </p>
<ul>
<li> A (undirected simple) <i>graph</i> <i>G</i> consists of a set <i>V</i> of <a href="http://en.wikipedia.org/wiki/Vertex_(graph_theory)" target="_blank" title="Vertex (graph theory)"><i>vertices</i></a> (aka <i>nodes</i>) and a set <i>E</i> of pairs of vertices called <i>edges</i>; thus <i>G</i> = (<i>V</i>, <i>E</i>). </li>
<li> A <a href="http://goldbook.iupac.org/terms/view/MT07069" target="_blank" title="molecular graph in Gold Book"><i>molecular graph</i></a> is a (undirected simple) graph whose vertices <i>V</i> correspond to the atoms and edges <i>E</i> correspond to bonds. </li>
<li> The <i>order</i> of a graph is its number of vertices |<i>V</i>|; therefore, the order of a molecular graph is the same as the number of atoms<sup>*</sup>. </li>
<li> The <i>size</i> of a graph is its number of edges |<i>E</i>|, i.e. number of bonds. </li>
<li> The <a href="http://en.wikipedia.org/wiki/Degree_(graph_theory)" target="_blank" title="Degree (graph theory) in Wikipedia"><i>degree</i></a> (or <i>valency</i>) of a vertex is its number of <a href="http://en.wikipedia.org/wiki/Incidence_(graph)" target="_blank" title="Incidence (graph) in Wikipedia">incident</a> edges; accordingly, the degree of an atom in a molecular graph is the number of distinct bonds attached to it. </li>
<li> Two edges are <i>adjacent</i> if they share a common vertex. </li>
<li> Two vertices are <i>adjacent</i> if they share a common edge. </li>
<li> A <i>subgraph</i> of a graph <i>G</i> is another graph <i>G</i>′ formed from a subset of the vertices and edges of <i>G</i>. </li>
<li> A <i>walk</i> is a sequence of edges (i.e. bonds) which joins a sequence of vertices (i.e. atoms). </li>
<li> A <i>trail</i> is a walk in which all edges (i.e. bonds) are distinct. </li>
<li> A <a href="http://en.wikipedia.org/wiki/Path_(graph_theory)" target="_blank" title="Path (graph theory) in Wikipedia"><i>path</i></a> is a trail in which all vertices (i.e. atoms) are distinct. </li>
<li> A <a href="http://en.wikipedia.org/wiki/Cycle_(graph_theory)" target="_blank" title="Cycle (graph theory) in Wikipedia"><i>cycle</i></a> is a trail in which the only repeated vertices are the first and last vertices. </li>
<li> A <a href="http://en.wikipedia.org/wiki/Cycle_graph" target="_blank" title="Cycle graph in Wikipedia"><i>cycle graph</i></a> is a graph that consists of a single cycle. </li>
<li> An <i>acyclic graph</i> is a graph without cycles. </li>
<li> A <a href="http://en.wikipedia.org/wiki/Connectivity_(graph_theory)" target="_blank" title="Connectivity (graph theory) in Wikipedia"><i>connected</i></a> graph is an undirected graph in which every pair of vertices is joined by a path. </li>
<li> A <a href="http://en.wikipedia.org/wiki/Tree_(graph_theory)" target="_blank" title="Tree (graph theory) in Wikipedia"><i>tree</i></a> is a connected acyclic graph. </li>
<li> A <i>unicyclic graph</i> or <i>1-tree</i> is a connected graph that contains a single cycle. </li>
</ul>
<p> Diestel [1, pp. 6—7] defines path and cycle as follows: </p>
<ul>
<li> A <i>path</i> from vertex <i>x</i><sub>0</sub> to vertex <i>x</i><sub><i>k</i></sub> is a non-empty graph <i>P</i><sup><i>k</i></sup> = (<i>V</i>,<i>E</i>) of the form <br />
<i>V</i> = {<i>x</i><sub>0</sub>, <i>x</i><sub>1</sub>, ..., <i>x</i><sub><i>k</i></sub>}; <i>E</i> = {<i>x</i><sub>0</sub><i>x</i><sub>1</sub>, <i>x</i><sub>1</sub><i>x</i><sub>2</sub>, ..., <i>x</i><sub><i>k</i>−1</sub><i>x</i><sub><i>k</i></sub>} <br />
where the <i>x</i><sub><i>i</i></sub> are all distinct. </li>
<li> The number of edges of a path is its <i>length</i>. </li>
</ul>
<p> Hence the length <i>k</i> of the path <i>P</i><sup><i>k</i></sup> is equal to its size |<i>E</i>|; its order |<i>V</i>| = <i>k</i>+1. </p>
<ul>
<li> A <i>cycle</i> is the graph <i>C</i><sup><i>k</i></sup> = <i>P</i><sup><i>k</i>−1</sup> + <i>x</i><sub><i>k</i>−1</sub><i>x</i><sub>0</sub>, where <i>k</i>≥3. </li>
<li> The <i>length</i> of a cycle is its number of edges (or vertices). </li>
</ul>
<p> Thus the length <i>k</i> of the cycle <i>C</i><sup><i>k</i></sup> is equal to its size |<i>E</i>| and its order |<i>V</i>|. </p>
<p> So we can define a <i>chain</i> (in chemical sense) as </p>
<table width="90%">
<tr>
<td width="90%"><blockquote> a path consisting of at least two adjacent edges (bonds) linking at least three vertices (atoms), or <br />
<i>P</i><sup><i>k</i></sup> where <i>k</i>≥2. </blockquote> </td>
<td align="right" width="10%"><b>(4)</b></td>
</tr>
</table>
<p> García-Domenech <i>et al</i>. [2] provide an alternative: </p>
<table width="90%">
<tr>
<td width="90%"><blockquote> End vertices are called <i>terminals</i>, and a tree with two terminals is called a <i>chain</i>. </blockquote> </td>
<td align="right" width="10%"><b>(5)</b></td>
</tr>
</table>
<p> Both definitions <b>(4)</b> and <b>(5)</b> imply that the chain is unbranched. Is it so? Let’s come back to hexane <b>(a)</b>: </p>
<p><center><a href="http://commons.wikimedia.org/wiki/File:Hexane-2D-Skeletal.svg" target="_blank" title="Skeleton diagram of a hexane molecule @ Wikimedia"><img height="50" src="http://upload.wikimedia.org/wikipedia/commons/thumb/6/6b/Hexane-2D-Skeletal.svg/1280px-Hexane-2D-Skeletal.svg.png" width="200" /></a></center></p>
<p> This is a typical representation of unbranched carbon chain. Even so, we know that in reality there are also hydrogen atoms. Here’s how a complete structural formula of hexane looks like: </p>
<p><center><a href="http://commons.wikimedia.org/wiki/File:Hexane-2D-B.png" target="_blank" title="Structural formula of hexane @ Wikimedia"><img height="93" src="http://upload.wikimedia.org/wikipedia/commons/d/d3/Hexane-2D-B.png" width="200" /></a></center></p>
<p> So the whole thing is not a chain but a tree. What shall we do? </p>
<p> Well, we can define a <i>carbon chain</i> or <i>carbochain</i> as a chain in which all vertices are carbon atoms. So for carbon-containing molecules a carbon chain is a subgraph of a molecular graph. We can further expand this definition to <i>all</i> non-hydrogen atoms and call it, say, a <i>hydrogenless chain</i>, although I don’t expect many people to like this name. Alternatively, we can start with <a href="http://en.wikipedia.org/wiki/Molecular_graph" target="_blank" title="Molecular graph in Wikipedia"><i>hydrogen-depleted</i></a>, or <i>hydrogen-suppressed</i>, graphs, i.e. the molecular graphs with hydrogen vertices deleted, and then proceed with looking for chains. </p>
<p> Similarly, the complete structure of cyclohexane <b>(b)</b> is not a cycle graph but a 1-tree. We can define a <i>carbocycle</i> as a cycle in which all vertices are carbon atoms; define a <i>hydrogenless cycle</i> as a cycle in which all vertices are atoms other than hydrogen; or look for cycles in hydrogen-depleted graphs. The structure of diborane(6) <b>(f)</b> is also a 1-tree but in this case we cannot ignore hydrogens because then we’ll lose the cycle. </p>
<p> I just noticed that I used the term “unbranched” without defining it. What’s that? </p>
<p> We can define <i>branching point</i> of a graph as a vertex with a degree more than 2. In a molecular graph, that corresponds to an atom connected to more than two other atoms. Once again, organic chemists may want to disregard hydrogens, so we can accordingly modify our definition for carbon chains/hydrogenless chains and so on. Thus, <i>unbranched</i> graph is a graph that has no branching points. Although the definitions <b>(4)</b> and <b>(5)</b> render the phrase “unbranched chain” tautological, it is in wide use. </p>
<p> The beginning and end of the path could be chosen arbitrarily. Consequently, a part <i>P</i>′ of a cycle <i>C</i> could be legitimately considered a chain, provided it consists of at least two adjacent edges: </p>
<ul>
<i>P</i>′ = (<i>V</i>′,<i>E</i>′) <br />
<i>V</i>′ = {<i>x</i><sub><i>i</i></sub>, ..., <i>x</i><sub><i>j</i></sub>};
<i>E</i>′ = {<i>x</i><sub><i>i</i></sub><i>x</i><sub><i>i</i>+1</sub>, ..., <i>x</i><sub><i>j−1</i></sub><i>x</i><sub><i>j</i></sub>} <br />
where |<i>E</i>′|≥2.
</ul>
<p> One could find this useful when talking about macrocycles<sup>†</sup>. </p>
<p> Curiously, IUPAC came very close to defining chains and rings in inorganic structures [3]. However, in those recommendations, it is graphs that are defined in terms of chains and rings rather than the other way round. For instance, an acyclic graph is defined as </p>
<blockquote> an unbranched chain of nodes, or two or more unbranched chains of nodes connected to each other without formation of a cyclic structure. </blockquote>
<p> I hope in some future IUPAC recommendations they’ll get that right. </p>
<p> What about “<a href="http://en.wikipedia.org/wiki/Side_chain" target="_blank" title="Side chain in Wikipedia">side chain</a>”, a term widely used in polymer science and biochemistry? There are side chains and there are side chains, but all of them imply the existence of “main chain”, or <a href="http://en.wikipedia.org/wiki/Backbone_chain" target="_blank" title="Backbone chain in Wikipedia">backbone</a>. </p>
<p> In polymer science, the backbone is just the longest chain of the macromolecule and side chains are the branches. Only few polymers, e.g. <a href="http://en.wikipedia.org/wiki/Polyethylene" target="_blank" title="Polyethylene in Wikipedia">polyethylene</a>, consist of chains that fit our definition of (unbranched) carbon chain. Other polymers consist of sequences of <a href="http://goldbook.iupac.org/terms/view/C01288" target="_blank" title="constitutional unit in Gold Book">constitutional units</a> that could be intrinsically branched, like <a href="http://en.wikipedia.org/wiki/Polypropylene" target="_blank" title="Polypropylene in Wikipedia">polypropylene</a>, or contain cycles, like <a href="http://en.wikipedia.org/wiki/Polythiophene" target="_blank" title="Polythiophene in Wikipedia">polythiophene</a>. The way around this is to “contract” the constitutional units into special types of vertices, called “contraction nodes” [3] or “<a href="http://www.qmul.ac.uk/sbcs/iupac/phane/PhI1.html#p13" target="_blank" title="PhI-1.3. Superatom and Superatom Locant @ Phane Nomenclature, Part I: Phane Parent Names (Recommendations 1998)">superatoms</a>” [4]. Then we can still define the chain as </p>
<table width="90%">
<tr>
<td width="90%"><blockquote> a path consisting of at least two adjacent edges (bonds) linking at least three vertices (either atoms or superatoms). </blockquote> </td>
<td align="right" width="10%"><b>(4′)</b></td>
</tr>
</table>
<p> In biopolymers such as nucleic acids or polysaccharides, <i>all</i> constitutional units contain rings, so “contracting” them is really necessary if we want to treat them as chains. In proteins and peptides, it is customary to refer to the sequence –NH–C<sup>α</sup><sub><i>i</i></sub>–C(O)–NH–C<sup>α</sup><sub><i>i</i>+1</sub>–C(O)– ... as “backbone” and to the groups R<sub><i>i</i></sub>, R<sub><i>i</i>+1</sub>, etc. attached to C<sup>α</sup> atoms as “side chains”, although some of the latter hardly qualify: the side chain of glycine is just a hydrogen atom. </p>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> Not to be confused with <a href="http://en.wikipedia.org/wiki/Bond_order" target="_blank" title="Bond order in Wikipedia">bond order</a>. </td>
</tr>
<tr><td valign="top">†</td>
<td> A note 2 to the <a href="http://goldbook.iupac.org/terms/view/C00946" target="_blank" title="chain (in polymers) in Gold Book">Gold Book definition</a> <b>(1)</b> says that “a cyclic macromolecule has no end groups but may nevertheless be regarded as a chain”. </td></tr>
</table>
<h4> References </h4>
<ol>
<li> Diestel, R. <i>Graph Theory</i> (2nd ed.). Springer-Verlag, New York, 2000. </li>
<li> García-Domenech, R., Gálvez, J., de Julián-Ortiz, J.V. and Pogliani, L. (2008) Some new trends in chemical graph theory. <a href="http://doi.org/10.1021/cr0780006" target="_blank" title="García-Domenech et al. (2008) Chem. Rev. 108, 1127-1169."><i>Chemical Reviews</i> <b>108</b>, 1127—1169</a>. </li>
<li> Fluck, E.O. and Laitinen, R.S. (1997) Nomenclature of inorganic chains and ring compounds (IUPAC Recommendations 1997). <a href="http://doi.org/10.1351/pac199769081659" target="_blank" title="Fluck and Laitinen (1997) Pure Appl. Chem. 69, 1659-1692."><i>Pure and Applied Chemistry</i> <b>69</b>, 1659—1692</a>. </li>
<li> Powell, W.H. (1998) Phane nomenclature Part I: Phane parent names (IUPAC Recommendations 1998). <a href="http://doi.org/10.1351/pac199870081513" target="_blank" title="Powell (1998) Pure Appl. Chem. 70, 1513-1545."><i>Pure and Applied Chemistry</i> <b>70</b>, 1513—1545</a>. </li>
</ol>
Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-26020727533396129732021-01-09T23:00:00.025+00:002023-08-07T10:14:20.667+01:00Irregularity and suppletion<p> Now that we’ve established that all chemical names consist of <a href="http://metallome.blogspot.com/2020/10/content-morphemes.html" target="_blank" title="Content morphemes @ this blog">content words</a> and each content word includes at least one <a href="http://metallome.blogspot.com/2020/12/stems-roots-bases.html" target="_blank" title="Stems, roots, bases @ this blog">base</a>, we can rephrase our <a href="http://metallome.blogspot.com/2020/10/content-morphemes.html" target="_blank" title="Content morphemes @ this blog">original statement ix</a> </p>
<ol start="9" type="i">
<li> New chemical names are formed by combining existing content morphemes with functional morphemes or adding new content morphemes </li>
</ol>
<p> as </p>
<ol start="9" type="i">
<li> New chemical names are formed by combining existing bases with functional morphemes or adding new bases. </li>
</ol>
<p> When we say “combining”, we mean that the parts of our construction set themselves are not changing. Right? In this way, the chemical name-building (out of standardised blocks, like names of atoms, groups, etc.) reflects the actual molecule-building (out of standard blocks, like atoms, groups, etc.). </p>
<p> On the other hand, if we agree that chemical names <a href="http://metallome.blogspot.com/2020/10/step-back.html" target="_blank" title="Step back @ this blog">form part of a natural language</a>, we also have to accept that sometimes they behave in not quite regular fashion. For example, we can figure out that the substituent group called <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37603" target="_blank" title="vinyl group (CHEBI:37603)">ethenyl</a> is derived from <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16716" target="_blank" title="ethene (CHEBI:18153)">ethene</a> because they share the base ‘ethen’. However, we cannot deduce in the similar fashion that <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30396" target="_blank" title="phenyl group (CHEBI:30396)">phenyl group</a> is derived from <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16716" target="_blank" title="benzene (CHEBI:16716)">benzene</a>. What’s going on here? </p>
<a name='more'></a>
<p> This is a case of <a href="http://en.wikipedia.org/wiki/Suppletion" target="_blank" title="Suppletion in Wikipedia"><i>suppletion</i></a>, which could be defined as the use of etymologically unrelated words within the same paradigm. Suppletion in a strict sense refers to different inflections of the word having unrelated stems, as can be observed in the conjugation of some irregular verbs (cf. English <i>go</i> and <i>went</i>, Spanish <i>ir</i>/<i>va</i>/<i>fue</i>, Russian идти/шёл and so on) or comparative and superlative forms of adjectives such as <i>good</i> and <i>bad</i> (cf. English <i>good</i>/<i>better</i> and <i>bad</i>/<i>worse</i>, Spanish <i>bueno</i>/<i>mejor</i> and <i>malo</i>/<i>peor</i>, Russian хороший/лучший and плохой/худший, etc.) In a broader sense, suppletion encompasses similar processes within the <a href="http://en.wikipedia.org/wiki/Word_family" target="_blank" title="Word family in Wikipedia">word family</a>. For instance, English adjectives of frequency can be derived from the corresponding nouns, as in every <b>hour</b> → <b>hour</b>ly, every <b>day</b> → <b>dai</b>ly, every <b>week</b> → <b>week</b>ly, every <b>month</b> → <b>month</b>ly, every <i>two</i> <b>month</b>s → bi<b>month</b>ly... And then the pattern breaks down and gets replaced by a different one: every three <b>month</b>s → <u>quarter</u>ly, twice a <b>year</b> → bi<u>ann</u>ual, every <b>year</b> → <u>ann</u>ual, every <i>two</i> <b>year</b>s → bi<u>enn</u>ial, every <i>four</i> <b>year</b>s → quadr<u>enn</u>ial, etc. In this new pattern, the English roots are replaced by their Latin counterparts. </p>
<p> Let’s have a look now at some paradigms in chemical terminology, starting with element names and terms directly derived from them. In a perfectly regular paradigm, </p>
<ul>
<li> the English name is exactly the same as the Latin name, or at least they share the base; </li>
<li> the derived terms for anions, <a href="http://metallome.blogspot.com/p/parent-names-of-mononuclear-hydrides.html" target="_blank" title="Parent names of mononuclear hydrides @ this blog">parent hydrides</a>, groups, ligands etc. share the same base; </li>
<li> the element symbol shares the first letter with the element name; in case of two-letter symbols, the second letter is also found in the element name. </li>
</ul>
<p> Like here [1, pp. 337—339]: </p>
<center><table width="90%">
<tr><th>Element symbol</th> <th align="left">Latin name</th> <th align="left">English name</th> <th align="left">Monoatomic anion</th> <th align="left">Heteroatomic anion</th> <th align="left">‘a’ term</th> <th align="left">‘y’ term</th> <th align="left">Hydride</th></tr>
<tr><th align="center">Cr</th> <td><b>chrom</b>ium</td> <td><b>chrom</b>ium</td> <td><b>chrom</b>ide</td> <td><b>chrom</b>ate</td> <td><b>chrom</b>a</td> <td><b>chrom</b>y</td> <td>—</td></tr>
<tr><th align="center">Ga</th> <td><b>gall</b>ium</td> <td><b>gall</b>ium</td> <td><b>gall</b>ide</td> <td><b>gall</b>ate</td> <td><b>gall</b>a</td> <td><b>gall</b>y</td> <td><b>gall</b>ane</td> </tr>
<tr><th align="center">I</th> <td><b>iod</b>um</td> <td><b>iod</b>ine</td> <td><b>iod</b>ide</td> <td><b>iod</b>ate</td> <td><b>iod</b>a</td> <td><b>iod</b>y</td> <td><b>iod</b>ane</td> </tr>
<tr><th align="center">P</th> <td><b>phosph</b>orus</td> <td><b>phosph</b>orus</td> <td><b>phosph</b>ide</td> <td><b>phosph</b>ate; <b>phosph</b>ite </td> <td><b>phosph</b>a</td> <td><b>phosph</b>y</td> <td><b>phosph</b>ane</td> </tr>
<tr><th align="center">Xe</th> <td><b>xenon</b>ium</td> <td><b>xenon</b></td> <td><b>xenon</b>ide</td> <td><b>xenon</b>ate</td> <td><b>xenon</b>a</td> <td><b>xenon</b>y</td> <td>—</td></tr>
</table></center>
<p> Now and then, however, you’ll see deviations from this paradigm. In case of silicon and germanium, their corresponding bases, ‘silic’ and ‘german’, are conserved in the names of anions but get shortened to ‘sil’ and ‘germ’ in the names of hydrides and in the ‘a’ and ‘y’ terms. Carbon keeps the base ‘carbon’ in the name of heteroatomic anion, carbonate, otherwise it is shortened to ‘carb’. Aluminium, selenium, tellurium and polonium conserve their bases ‘alumin’, ‘selen’, ‘tellur’ and ‘polon’ throughout except for the names of hydrides where they get truncated to ‘alum’, ‘sel’, ‘tell’ and ‘pol’, respectively. The opposite story is with indium: all the derived terms contain the root ‘ind’ which gets an extension in the hydride name indigane<sup>*</sup>. Hydrogen and oxygen contain two roots each, ‘hydr’/‘ox’ and ‘gen’. The second root is lost everywhere except for the heteroatomic anion names, hydrogenate and oxygenate. The origin of the suffix ‘on’ in ‘hydrony’ is unclear (<a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15378" target="_blank" title="hydron (CHEBI:15378)">hydron</a> is the general name of the ion H<sup>+</sup>). The name oxidane, uniquely for inorganic hydrides, contains the suffix ‘id’<sup>†</sup>. </p>
<center><table width="90%">
<tr><th>Element symbol</th> <th align="left">Latin name</th> <th align="left">English name</th> <th align="left">Monoatomic anion</th> <th align="left">Heteroatomic anion</th> <th align="left">‘a’ term</th> <th align="left">‘y’ term</th> <th align="left">Hydride</th></tr>
<tr><th align="center">Al</th> <td><u><b>alum</b>in</u>ium</td> <td><u><b>alum</b>in</u>ium</td> <td><u><b>alum</b>in</u>ide</td> <td><u><b>alum</b>in</u>ate</td> <td><u><b>alum</b>in</u>a</td> <td><u><b>alum</b>in</u>y</td> <td><b>alum</b>ane</td> </tr>
<tr><th align="center">In</th> <td><b>ind</b>ium</td> <td><b>ind</b>ium</td> <td><b>ind</b>ide</td> <td><b>ind</b>ate</td> <td><b>ind</b>a</td> <td><b>ind</b>y</td> <td><b>ind</b><u>ig</u>ane</td> </tr>
<tr><th align="center">C</th> <td><u><b>carb</b>on</u>ium</td> <td><u><b>carb</b>on</u></td> <td><b>carb</b>ide</td> <td><u><b>carb</b>on</u>ate</td> <td><b>carb</b>a</td> <td><b>carb</b>y</td> <td><b>carb</b>ane</td> </tr>
<tr><th align="center">Si</th> <td><u><b>sil</b>ic</u>ium</td> <td><u><b>sil</b>ic</u>on</td> <td><u><b>sil</b>ic</u>ide</td> <td><u><b>sil</b>ic</u>ate</td> <td><b>sil</b>a</td> <td><b>sil</b>y</td> <td><b>sil</b>ane</td> </tr>
<tr><th align="center">Ge</th> <td><u><b>germ</b>an</u>ium</td> <td><u><b>germ</b>an</u>ium</td> <td><u><b>germ</b>an</u>ide</td> <td><u><b>germ</b>an</u>ate</td> <td><b>germ</b>a</td> <td><b>germ</b>y</td> <td><b>germ</b>ane</td> </tr>
<tr><th align="center">H</th> <td><u><b>hydr</b>ogen</u>ium</td> <td><u><b>hydr</b>ogen</u></td> <td><b>hydr</b>ide</td> <td><u><b>hydr</b>ogen</u>ate</td> <td>—</td> <td><b>hydr</b>ony</td> <td>—</td> </tr>
<tr><th align="center">O</th> <td><u><b>ox</b>ygen</u>ium</td> <td><u><b>ox</b>ygen</u></td> <td><b>ox</b>ide</td> <td><u><b>ox</b>ygen</u>ate</td> <td><b>ox</b>a</td> <td><b>ox</b>y</td> <td><b>ox</b>idane</td> </tr>
<tr><th align="center">Se</th> <td><u><b>sel</b>en</u>ium</td> <td><u><b>sel</b>en</u>ium</td> <td><u><b>sel</b>en</u>ide</td> <td><u><b>sel</b>en</u>ate; <u><b>sel</b>en</u>ite </td> <td><u><b>sel</b>en</u>a</td> <td><u><b>sel</b>en</u>y</td> <td><b>sel</b>ane</td> </tr>
<tr><th align="center">Te</th> <td><u><b>tell</b>ur</u>ium</td> <td><u><b>tell</b>ur</u>ium</td> <td><u><b>tell</b>ur</u>ide</td> <td><u><b>tell</b>ur</u>ate</td> <td><u><b>tell</b>ur</u>a</td> <td><u><b>tell</b>ur</u>y</td> <td><b>tell</b>ane</td> </tr>
<tr><th align="center">Po</th> <td><u><b>pol</b>on</u>ium</td> <td><u><b>pol</b>on</u>ium</td> <td><u><b>pol</b>on</u>ide</td> <td><u><b>pol</b>on</u>ate</td> <td><u><b>pol</b>on</u>a</td> <td><u><b>pol</b>on</u>y</td> <td><b>pol</b>ane</td> </tr>
</table></center>
<p> So what, you might say. In spite of these irregularities, one still can deduce the meaning of derived terms. But wait. For iron, copper, silver, gold, lead and tin — six of <a href="http://en.wikipedia.org/wiki/Metals_of_antiquity" target="_blank" title="Metals of antiquity in Wikipedia">seven classical metals</a> — both the element symbols and all the derived terms come from Latin, including the <a href="http://metallome.blogspot.com/p/parent-names-of-mononuclear-hydrides.html" target="_blank" title="Parent names of mononuclear hydrides @ this blog">hydride names</a> for lead and tin. On the other extreme, <i>hydrargyrum</i>, the Latin name for mercury, has left its trace only in the element symbol, Hg. All the derived terms contain the root ‘mercur’, which unfortunately results in the ‘y’ term being identical to the element name. In case of antimony, another element which ends in ‘-y’, we have an intermediate situation: the anion names, antimonide and antimonate, keep the English root ‘antimon’ whereas the ‘a’ and ‘y’ terms as well as the element symbol Sb are based on the Latin name <i>stibium</i>. With nitrogen, the anion names are nitride, nitrate and nitrite although the ‘a’ and ‘y’ terms are derived from the French <i>azote</i>. Sulfur is almost regular except for the ‘a’ term, ‘thia’, from the Greek θεῖον. </p>
<p> IUPAC was pushing to make the situation with sodium, potassium and tungsten the same as with mercury: completely regular except for the element symbols. The 2005 edition of Red Book discards ‘kalide’ and ‘natride’ as obsolete and recommends ‘potasside’ and ‘sodide’, respectively. It also gets rid of all words with the root ‘wolfram’ although the earlier publications recommended the terms ‘wolframate’ [2] and ‘wolframy’ [3]. Given that in Latin, Spanish, Nordic and Slavic languages the name of this element is a variation on German <a href="http://en.wiktionary.org/wiki/Wolfram" target="_blank" title="Wolfram in Wiktionary"><i>Wolfram</i></a>, it’s little wonder that chemists expressed their concern about disappearance of ‘wolfram’ as an acceptable alternative to tungsten [4]. </p>
<center><table width="90%">
<tr><th>Element symbol</th> <th align="left">Latin name</th> <th align="left">English name</th> <th align="left">Monoatomic anion</th> <th align="left">Heteroatomic anion</th> <th align="left">‘a’ term</th> <th align="left">‘y’ term</th> <th align="left">Hydride</th></tr>
<tr><th align="center">Ag</th> <td><b>argent</b>um</td> <td>silver</td> <td><b>argent</b>ide</td> <td><b>argent</b>ate</td> <td><b>argent</b>a</td> <td><b>argent</b>y</td> <td>—</td></tr>
<tr><th align="center">Au</th> <td><b>aur</b>um</td> <td>gold</td> <td><b>aur</b>ide</td> <td><b>aur</b>ate</td> <td><b>aur</b>a</td> <td><b>aur</b>y</td> <td>—</td></tr>
<tr><th align="center">Cu</th> <td><b>cupr</b>um</td> <td>copper</td> <td><b>cupr</b>ide</td> <td><b>cupr</b>ate</td> <td><b>cupr</b>a</td> <td><b>cupr</b>y</td> <td>—</td></tr>
<tr><th align="center">Fe</th> <td><b>ferr</b>um</td> <td>iron</td> <td><b>ferr</b>ide</td> <td><b>ferr</b>ate</td> <td><b>ferr</b>a</td> <td><b>ferr</b>y</td> <td>—</td></tr>
<tr><th align="center">Hg</th> <td><b>hydrargyr</b>um</td> <td><u>mercur</u>y</td> <td><u>mercur</u>ide</td> <td><u>mercur</u>ate</td> <td><u>mercur</u>a</td> <td><u>mercur</u>y</td> <td>—</td></tr>
<tr><th align="center">K</th> <td><b>kal</b>ium</td> <td><u>potass</u>ium</td> <td><b>kal</b>ide <br /> <u>potass</u>ide </td> <td><u>potass</u>ate</td> <td><u>potass</u>a</td> <td><b>kal</b>y <br /> <u>potass</u>y</td> <td>—</td></tr>
<tr><th align="center">Na</th> <td><b>natr</b>ium</td> <td><u>sod</u>ium</td> <td><b>natr</b>ide <br /> <u>sod</u>ide </td> <td><u>sod</u>ate</td> <td><u>sod</u>a</td> <td><b>natr</b>y <br /> <u>sod</u>y</td> <td>—</td></tr>
<tr><th align="center">Pb</th> <td><b>plumb</b>um</td> <td>lead</td> <td><b>plumb</b>ide</td> <td><b>plumb</b>ate</td> <td><b>plumb</b>a</td> <td><b>plumb</b>y</td> <td><b>plumb</b>ane</td></tr>
<tr><th align="center">Sb</th> <td><b>stib</b>ium</td> <td><u>antimon</u>y</td> <td><u>antimon</u>ide</td> <td><u>antimon</u>ate</td> <td><b>stib</b>a</td> <td><b>stib</b>y</td> <td><b>stib</b>ane</td></tr>
<tr><th align="center">Sn</th> <td><b>stann</b>um</td> <td>tin</td> <td><b>stann</b>ide</td> <td><b>stann</b>ate</td> <td><b>stann</b>a</td> <td><b>stann</b>y</td> <td><b>stann</b>ane</td></tr>
<tr><th align="center">W</th> <td><b>wolfram</b>ium</td> <td><u>tungst</u>en</td> <td><u>tungst</u>ide</td> <td><b>wolfram</b>ate <br /> <u>tungst</u>ate</td> <td><u>tungst</u>a</td> <td><b>wolfram</b>y <br /> <u>tungst</u>y</td> <td>—</td></tr>
<tr><th></th> <th>French name</th> <th></th> <th></th> <th></th> <th></th> <th></th></tr>
<tr><th align="center">N</th> <td><b>az</b>ote </td> <td><u>nitr</u>ogen</td> <td><u>nitr</u>ide</td> <td><u>nitr</u>ate; <u>nitr</u>ite </td> <td><b>az</b>a</td> <td><b>az</b>y</td> <td><b>az</b>ane</td></tr>
<tr><th></th> <th>Greek name</th> <th></th> <th></th> <th></th> <th></th> <th></th></tr>
<tr><th align="center">S</th> <td>θεῖον (<b>thei</b>on) </td> <td><u>sulf</u>ur</td> <td><u>sulf</u>ide</td> <td><u>sulf</u>ate; <u>sulf</u>ite </td> <td><b>thi</b>a</td> <td><u>sulf</u>y</td> <td><u>sulf</u>ane</td></tr>
</table></center>
<p> Another paradigm is at the core of <a href="http://metallome.blogspot.com/2020/06/substitutive-names-and-parent-hydrides.html" target="_blank" title="Substitutive names and parent hydrides @ this blog">substitutive nomenclature</a>. The names of the substituents can either precede the name of the parent structure, in which case they are (incorrectly) referred to as “<a href="http://metallome.blogspot.com/2020/10/prefixes-or-combining-forms.html" target="_blank" title="Prefixes — or combining forms? @ this blog">prefixes</a>”, or follow it, as “<a href="http://metallome.blogspot.com/2020/12/suffixes-or-combining-forms.html" target="_blank" title="Suffixes — or combining forms? @ this blog">suffixes</a>”. In fact the names of the substituents are combining forms which contain at least one root.
In any given structure, one — and only one — of the substituents can be chosen as the <a href="http://goldbook.iupac.org/terms/view/P04846" target="_blank" title="principal group in Gold Book">principal group</a>, i.e. group that gives the name to the class. This substituent will occupy the place of “suffix”, while the rest can only be “prefixes”. You’d be right to expect the names of the substituents to share their roots/bases no matter where they are positioned. Indeed, here’s how the “regular” substituents behave [5]: </p>
<center><table width="50%">
<tr><th align="left">Formula</th> <th align="left">Class</th> <th align="left">“Suffix”</th> <th align="left">“Prefix”</th> </tr>
<tr><td>–COO<sup>−</sup></td> <td><b>carboxylat</b>es</td> <td>-<b>carboxylat</b>e</td> <td><b>carboxylat</b>o-</td> </tr>
<tr><td>–COOH</td> <td><b>carboxy</b>lic acids</td> <td>-<b>carboxy</b>lic acid</td> <td><b>carboxy</b>-</td> </tr>
<tr><td>–NH<sub>2</sub></td> <td><b>amin</b>es</td> <td>-<b>amin</b>e</td> <td><b>amin</b>o-</td> </tr>
<tr><td>=NH</td> <td><b>imin</b>es</td> <td>-<b>imin</b>e</td> <td><b>imin</b>o-</td> </tr>
<tr><td>–P(O)(OH)<sub>2</sub></td> <td><b>phosphon</b>ic acids</td> <td>-<b>phosphon</b>ic acid</td> <td><b>phosphon</b>o-</td> </tr>
<tr><td>–S(O)<sub>2</sub>–</td> <td><b>sulfon</b>es</td> <td>-<b>sulfon</b>e</td> <td><b>sulfon</b>yl-</td> </tr>
</table>
</center>
<p> In many cases, however, the “prefix” and “suffix” names for the same substituent have no common bases. In case of –SH group, there are even <i>three</i> suppletive names: the perfectly regular “prefix” ‘sulfanyl-’, derived from the parent hydride name sulfane; another “prefix” ‘<a href="http://en.wiktionary.org/wiki/mercapto-" target="_blank" title="mercapto- in Wiktionary">mercapto</a>’, introduced by the Danish chemist <a href="http://en.wikipedia.org/wiki/William_Christopher_Zeise" target="_blank" title="William Christopher Zeise in Wikipedia">William Christopher Zeise</a>, from the Latin <i>mercurium captāns</i>, “capturing mercury” (“no longer acceptable” by IUPAC but still in wide use); and “suffix” ‘thiol’, which consists of Greek-derived root ‘thi’ plus ‘ol’ from ‘alcohol’. </p>
<center><table width="50%">
<tr><th align="left">Formula</th> <th align="left">Class</th> <th align="left">“Suffix”</th> <th align="left">“Prefix”</th> </tr>
<tr><td>–CHO</td> <td rowspan="2"><b>aldehyd</b>es</td> <td>-carb<b>aldehyd</b>e</td> <td>formyl-</td> </tr>
<tr><td>–{C}HO <sup>‡</sup></td> <td>-<b>al</b></td> <td>oxo-</td> </tr>
<tr><td>–C≡N</td> <td rowspan="2"><b>nitril</b>es</td> <td>-carbo<b>nitril</b>e</td> <td>cyano-</td> </tr>
<tr><td>–{C}≡N <sup>‡</sup></td> <td>-<b>nitril</b>e</td> <td>—</td> </tr>
<tr><td>=O</td> <td><b>keton</b>es</td> <td>-<b>keton</b>e</td> <td>oxo-</td> </tr>
<tr><td>–OH</td> <td>alcoh<b>ol</b>s</td> <td>-<b>ol</b></td> <td>hydroxo- </td> </tr>
<tr><td>–SH</td> <td><b>thiol</b>s</td> <td>-<b>thiol</b></td> <td>mercapto- <br /> sulfanyl-</td> </tr>
</table>
</center>
<p> Nevertheless, the “suffix”, if present, often shares the root, or a part thereof, with the corresponding class name. For instance, ‘alcohol’ gets shortened to ‘ol’ and ‘aldehyde’ to ‘al’. </p>
<p> Just like in natural languages, it is the most common words that tend to be irregular. Consider the molecule <b>(a)</b> known under its Germanic name ‘water’. The Latin word ‘aqua’ is used to designate water ligands, as in pentaaquanitrosyliron(2+) <b>(b)</b>, while ‘hydrate’, as in <b>(c)</b>, and <a href="http://metallome.blogspot.com/2020/07/subtractive-names.html" target="_blank" title="Subtractive names @ this blog">subtractive</a> ‘anhydro’ names contain the root ‘hydr’ (from Greek ὕδωρ). </p>
<center>
<table>
<tr>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="water (CHEBI:15377)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKUS83t8i_L1OVuBAXk6-qe0VGJF2IHbv7sMouGWezrmjoeuQA3tQwJm7f8qcpH5wzCXWWByCtX4xovY-BRU5Jut4iXMXVr8C4EtnFSLlPllAwhI_iEVyN7k76JJZRtYRUbgDXGg/w200-h200/water.png" width="200" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30994" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="pentaaquanitrosyliron(2+) (CHEBI:30994)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjauZ4TgNuZQ7gSGvbKXj68_caUMqwxl2w_H9d00Ge8lyir1Mihc1Gn3t0QGpnsBJ_Ka2zVF9KaNEsmGt_YtAIUPEjla9kef7U78w0SYTg135ET2wkYU_rX_8mWmR2973oH5UnY8Q/s1600/pentaaquanitrosyliron%2528II%2529.png" /></a></td>
<td><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:9179" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="sodium nitroprusside dihydrate (CHEBI:9179)"><img border="0" data-original-height="200" data-original-width="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgqVM3nBY44_knQUhmjhTuEiUvqO7B8fSzoaiNLdgxx-qytcsqQ7TzIDTjbL_n5VoMfomwo8ekI-TNL08F6YeBQCZmQYInPthJIkeFkkJnFi63qyQB1Fvo-hRLYfw9HnJvcIrukCg/s0/sodium_nitroprusside_dihydrate.png" /></a></td>
</tr>
<tr><th align="center">(a)</th> <th align="center">(b)</th> <th align="center">(c)</th>
</tr>
</table>
</center>
<center>
<table>
<tr>
<td><ol start="1" type="a">
<li> H<sub>2</sub>O <br />
water (<i>trivial</i>) <br />
oxidane (<i>parent hydride</i>) <br />
dihydrogen oxide (<i>binary</i>) <br />
dihydridooxygen (<i>additive</i>) </li>
<li> [Fe(NO)(OH<sub>2</sub>)<sub>5</sub>]<sup>2+</sup> <br />
pentaaquanitrosyliron(2+) (<i>additive</i>) </li>
<li> Na<sub>2</sub>[Fe(CN)<sub>5</sub>(NO)]·2H<sub>2</sub>O <br />
sodium pentacyanidonitrosylferrate(2−) dihydrate <br />
disodium pentacyanidonitrosylferrate—water (1/2) </li>
</ol>
</td>
</tr>
</table>
</center>
<table>
<tr><td colspan="2"><hr style="background-color: black; border-width: 0px; height: 0.5px; margin-left: 0px; text-align: left; width: 50%;" /></td></tr>
<tr><td valign="top">*</td>
<td> The name <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:37911" target="_blank" title="indane (CHEBI:37911)">indane</a> is “well established as the name of the hydrocarbon 2,3-dihydroindene” [1, p. 85]. </td>
</tr>
<tr><td valign="top">†</td>
<td> <a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:46941" target="_blank" title="oxane (CHEBI:46941)">Oxane</a> is a <a href="http://metallome.blogspot.com/2021/04/hantzsch-widman-names.html" target="_blank" title="Hantzsch-Widman names @ this blog">Hantzsch-Widman name</a> of 2<i>H</i>-tetrahydropyran [1, p. 85]. </td></tr>
<tr><td valign="top">‡</td>
<td> {C} indicates the carbon atom implicit in the parent name. </td>
</tr>
</table>
<h4> References </h4>
<ol>
<li> Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. <a href="http://old.iupac.org/publications/books/author/connelly.html" target="_blank" title="Nomenclature of Inorganic Chemistry @ IUPAC web site"><i>Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005</i></a>. Royal Society of Chemistry, Cambridge, 2005. </li>
<li> International Union of Pure and Applied Chemistry. <a href="http://publications.iupac.org/pac/28/1/index.html" target="_blank" title="Nomenclature of Inorganic Chemistry: Definitive Rules 1970 @ IUPAC"><i>Nomenclature of Inorganic Chemistry: Definitive Rules 1970.</i></a> Butterworths, London, 1971. </li>
<li> Fluck, E.O. and Laitinen, R.S. (1997) Nomenclature of inorganic chains and ring compounds (IUPAC Recommendations 1997). <a href="http://doi.org/10.1351/pac199769081659" target="_blank" title="Fluck and Laitinen (1997) Pure Appl. Chem. 69, 1659-1692."><i>Pure and Applied Chemistry</i> <b>69</b>, 1659—1692</a>. </li>
<li> Goya, P. and Román, P. (2005) Wolfram vs. Tungsten. <a href="http://doi.org/10.1515/ci.2005.27.4.26" target="_blank" title="Goya and Román (2005) Chem. Int. 27, 26-27"><i>Chemistry International</i> <b>27</b>, 26—27</a>. </li>
<li> Hellwich, K.-H., Hartshorn, R.M., Yerin, A., Damhus, T. and Hutton, A.T. (2020) Brief guide to the nomenclature of organic chemistry (IUPAC Technical Report). <a href="http://doi.org/10.1515/pac-2019-0104" target="_blank" title="Hellwich et al. (2020) Pure Appl. Chem. 92, 527-539."><i>Pure and Applied Chemistry</i> <b>92</b>, 527—539</a>. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0tag:blogger.com,1999:blog-11643254.post-35896275162145045652020-12-29T16:00:00.076+00:002023-09-24T14:06:54.842+01:00Stems, roots, bases<p> In a number of IUPAC publications, the entities that are referred to as “<a href="http://en.wikipedia.org/wiki/Word_stem" target="_blank" title="Word stem in Wikipedia">stems</a>” include </p>
<ul>
<li> Latin stems such as ‘argent’, ‘aur’, ‘cupr’, ‘ferr’, etc. used before ‘ide’ or ‘ate’ in anion names [1]; </li>
<li> Stem name ‘carotene’ in nomenclature of carotenoids [2, <a href="http://www.qmul.ac.uk/sbcs/iupac/carot/car1t7.html#p2" target="_blank" title="Nomenclature of Carotenoids: Carotenoid Rules 1 to 7">rule 2</a>]; </li>
<li> Stem ‘calci-’ in nomenclature of vitamin D [3]; </li>
<li> Stem ‘retin-’ in nomenclature of retinoids [4]; </li>
<li> In carbohydrate nomenclature, stem names that designate the chain length of the sugar, e.g. ‘pent-’, ‘hex-’, ‘hept-’ etc. [5]; </li>
<li> Stems such as ‘irene’, ‘irane’, ‘epine’ etc. in <a href="http://metallome.blogspot.com/2021/04/hantzsch-widman-names.html" target="_blank" title="Hantzsch-Widman names @ this blog">Hantzsch-Widman</a> (H-W) nomenclature [6]; </li>
<li> Stem name ‘phosphatidic acid’ [7]. </li>
</ul>
<p> Before we go any further, we have to distinguish between the terms “<a href="http://en.wikipedia.org/wiki/Root_(linguistics)" target="_blank" title="Root (linguistics) in Wikipedia">root</a>”, “stem” and “base”, which are often used interchangeably even in linguistic literature.
<a name='more'></a>
According to <a href="http://en.wikipedia.org/wiki/Laurie_Bauer" target="_blank" title="Laurie Bauer in Wikipedia">Laurie Bauer</a> [8], </p>
<blockquote> A <b>root</b> is a form which is not further analysable, either in terms of <a href="http://en.wikipedia.org/wiki/Morphological_derivation" target="_blank" title="Morphological derivation in Wikipedia">derivational</a> or <a href="http://en.wikipedia.org/wiki/Inflection" target="_blank" title="Inflection in Wikipedia">inflectional</a> morphology. It is that part of word-form that remains when all inflectional and derivational affixes have been removed. </blockquote>
<p> Here, I am going to stick to Bauer’s approach with one important modification: in addition to “all inflectional and derivational affixes”, I’d like to mention that <i>other roots</i> also have to be removed. For example, <b>sulf</b>ur, <b>sulf</b>ate, <b>sulf</b>ide, <b>sulf</b>ite, <b>sulf</b>o, <b>sulf</b>onic, <b>sulf</b>uric, peroxy<b>sulf</b>ate etc. all contain the root ‘sulf’. Most of the IUPAC examples above are single roots. </p>
<blockquote>A <b>stem</b> is of concern only when dealing with inflectional morphology. </blockquote>
<p> In other words, <a href="http://en.wikipedia.org/wiki/Word_stem" target="_blank" title="Word stem in Wikipedia">stem</a> is the part of a word that contains no inflectional affixes. Minimally, stem consists of a root. For example, <b>salt</b>, <b>salt</b>s, <b>salt</b>ed and <b>salt</b>ing all contain the stem <b>salt</b>, which in this case is identical with the root. Stems can also include derivational affixes, for example <b>desalt</b> = de- (prefix) + salt (root) or <b>salty</b> = salt (root) + -y (suffix), and may comprise more than one root, as in <b>saltpetre</b> or <b>saltwater</b>. </p>
<p> As there is very little inflection in English in general and in English chemical terminology in particular, we do not have much need to talk about “stems”. </p>
<blockquote> A <b>base</b> is any form to which affixes of any kind can be added. </blockquote>
<p> Again, I’d like to add <i>other roots</i> to Bauer’s definition. The H-W “stems” like ‘irene’ are always used in conjunction with element roots such as ‘az’, ‘bor’, ‘ox’, ‘sil’ and so on. So they are not really stems. They are not roots either as they are “further analysable”, for example, in ‘irene’ the root ‘ir’ means three-member cycle, ‘en’ indicates unsaturation and (optional) terminal ‘-e’ is the ending. The term “base” fits the bill here: </p>
<center>
<table>
<tr>
<td align="center" colspan="6"><a href="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30973" style="margin-left: 1em; margin-right: 1em;" target="_blank" title="oxirene (CHEBI:30973)"><img border="0" data-original-height="200" data-original-width="200" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAJW8OvrNfdu2zcWEBoYRajRUkbWD9oNdfYSvX9zbkCJaE47Mmkc_fAxn0RNcmAS5f3MjE1NzQCXCwOKBuLD4bO5MGksz4O4mCZOHJHTi8tTLJNliVvuU4MX_CCKJP3MfV_jnTHg/w200-h200/oxirene.png" width="200" /></a></td></tr>
<tr><th align="left">word:</th> <td align="center" colspan="5">oxirene</td></tr>
<tr><th align="left">stem:</th> <td align="center" colspan="3">oxiren</td> <th rowspan="3" valign="middle">ending:</th> <td align="center" rowspan="3" valign="middle">e</td></tr>
<tr><th align="left">base:</th> <td align="center">ox</td> <td align="center" colspan="2">iren</td></tr>
<tr><th align="left">root:</th> <td align="center">ox</td> <td align="center">ir</td> <td align="center">en</td> </tr></table>
</center>
<p> I understand the potential reluctance of chemists to use the word “base” as it has a few other meanings. However, when we are talking about the name formation, it’s hard to confuse it with other “bases”. </p>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tr><td style="text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikts1TGxfytpRgZ66U0ybm4n_wdlUE3BHfIzmFR3JzzfkbAtU_rdV_GKYaOMUWphyphenhyphennNg8dqC0yMDzlozo9fv4I0omLolLQEqcrWkvEubVsvgxd5ajCjvqqCIVaIwVvO2fhvyK48g/s1000/wordmetamodel.jpg" style="margin-left: 1em; margin-right: 1em;" title="The word meta-model diagram (courtesy of Heikki Lehväslaiho) created with https://plantuml.com/class-diagram
title Word meta-model
hide members
hide circle
class word
class stem
class base
class “derivational affix” as daffix
class “inflectional affix” as iaffix
class root
word o-- “1..*” stem
word o-- iaffix
stem - “0..*” iaffix
stem o-- “1..*” base : (longest)
base -right- “0..*” daffix
word o-- daffix
base o-- “1..*” root
class affix
class “derivational affix” as daffix2
class “inflectional affix” as iaffix2
affix <|-down- daffix2
affix <|-down- iaffix2"><img alt="The word meta-model diagram courtesy of Heikki Lehväslaiho" border="0" data-original-height="626" data-original-width="1000" height="250" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikts1TGxfytpRgZ66U0ybm4n_wdlUE3BHfIzmFR3JzzfkbAtU_rdV_GKYaOMUWphyphenhyphennNg8dqC0yMDzlozo9fv4I0omLolLQEqcrWkvEubVsvgxd5ajCjvqqCIVaIwVvO2fhvyK48g/w400-h250/wordmetamodel.jpg" width="400" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">The word meta-model diagram courtesy of <a href="http://about.me/heikki" target="_blank" title="Heikki's profile @ about.me">Heikki Lehväslaiho</a></td></tr></table>
<p> Lastly, it should be obvious that ‘phosphatidic acid’ [7] can be neither “stem” nor “base” for a simple reason that it’s not a part of a word but a noun phrase that consists of two separate words. In case of ‘phosphatidic’, its stem is identical to the complete word while containing a Russian-dollful of bases, each of them further modifiable with affixes and roots: ‘phosph’ (e.g. <b>phosph</b>ane), ‘phosphat’ (e.g. tri<b>phosphat</b>e), ‘phosphatid’ (e.g. <b>phosphatid</b>ylcholine), ‘phosphatidic’ (e.g. di<b>phosphatidic</b>). As for ‘acid’, its root, base and stem are all identical to the complete word. </p>
<center>
<table>
<tr><th align="left">phrase:</th> <td align="center" colspan="2">phosphatidic acid</td></tr>
<tr><th align="left">word:</th> <td>phosphatidic</td> <td align="center">acid</td> </tr>
<tr><th align="left">stem:</th> <td>phosphatidic</td> <td align="center">acid</td> </tr>
<tr><th align="left">base:</th> <td align="center">phosph / phosphat / phosphatid / phosphatidic</td> <td align="center">acid</td> </tr>
<tr><th align="left">root:</th> <td>phosph</td> <td align="center">acid</td> </tr></table>
</center>
<h4> References </h4>
<ol>
<li> Hartshorn, R.M., Hellwich, K.-H., Yerin, A., Damhus, T. and Hutton, A.T. (2015) Brief guide to the nomenclature of inorganic chemistry (IUPAC technical report). <a href="http://doi.org/10.1515/pac-2014-0718" target="_blank" title="Hartshorn et al. (2015) Pure Appl. Chem. 87(9-10), 1039-1049."><i>Pure and Applied Chemistry</i> <b>87</b>, 1039—1049</a>. </li>
<li> IUPAC and IUPAC-IUB (1975) Nomenclature of carotenoids (rules approved 1974). <a href="http://dx.doi.org/10.1351/pac197541030405" target="_blank" title="IUPAC and IUPAC-IUB (1974) Pure Appl. Chem. 41, 405-431."><i>Pure and Applied Chemistry</i> <b>41</b>, 405—431</a>. </li>
<li> IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) (1982) Nomenclature of vitamin D (Recommendations 1981). <a href="http://doi.org/10.1351/pac198254081511" target="_blank" title="JCBN (1982) Pure Appl. Chem. 54, 1511-1516."><i>Pure and Applied Chemistry</i> <b>54</b>, 1511—1516</a>. </li>
<li> IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) (1983) Nomenclature of retinoids. Recommendations 1981. <a href="http://doi.org/10.1351/pac198855040721" target="_blank" title="JCBN (1983) Pure Appl. Chem. 55, 721-726."><i>Pure and Applied Chemistry</i> <b>55</b>, 721—726</a>. </li>
<li> McNaught, A.D. (1996) Nomenclature of carbohydrates (IUPAC recommendations 1996). <i>Pure and Applied Chemistry</i> <b>68</b>, 1919—2008. <a href="http://www.qmul.ac.uk/sbcs/iupac/2carb/17.html" target="_blank" title="2-Carb-17. Unsaturated monosaccharides @ Nomenclature of carbohydrates">2-Carb-17. Unsaturated monosaccharides</a>. </li>
<li> Powell, W.H. (1983) Revision of the extended Hantzsch-Widman system of nomenclature for heteromonocycles (Recommendations 1982). <a href="http://doi.org/10.1351/pac198855020409" target="_blank" title="Powell (1983) Pure Appl. Chem. 55, 409-416."><i>Pure and Applied Chemistry</i> <b>55</b>, 409—416</a>. </li>
<li> IUPAC-IUB Commission on Biochemical Nomenclature (CBN) (1978) Nomenclature of lipids. Recommendations, 1976. <i>Biochem. J.</i> <b>171</b>, 21—35. <a href="http://www.qmul.ac.uk/sbcs/iupac/lipid/supp.html" target="_blank" title="Supplement: Derivatives of phosphatidic acid @ Nomenclature of Lipids">Supplement: Derivatives of phosphatidic acid</a>. </li>
<li> Bauer, L. (1983) <i>English Word-Formation</i>. Cambridge University Press, 1983, pp. 20—22. </li>
</ol>Kirillhttp://www.blogger.com/profile/00719435019715182189noreply@blogger.com0