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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head profile="http://gmpg.org/xfn/1"> <title>Computational Organic Chemistry » 2017 » January</title> <meta name="google-site-verification" content="g1Myv4tUVAmqRbwZeBi7IPuSZpP64RWjVJ6itIoouCo"> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <style type="text/css" media="screen">@import url( /blog/wp-content/themes/comporg/style.css);</style> <link rel="stylesheet" id="wp-block-library-css" href="/blog/wp-includes/css/dist/block-library/style.min.css?ver=5.6.1" type="text/css" media="all"> <script type="text/javascript">  </script> </head> <body> <div id="header"> <div id="header_img"></div> </div> <div id="link_section"> <div style="float:left"> <a href="/blog/about">About this Blog</a> | <a href="/">Book Homepage</a> | <a href="http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471713422.html">Purchase the Book</a> </div> </div> <div id="after_links"></div> <div id="content"> <div id="main"> <h2 class="post-title">Archive for January, 2017</h2> <div class="box"> <h2><a href="/blog/archives/3929" rel="bookmark" title="Permanent Link: A six-coordinate carbon atom">A six-coordinate carbon atom</a></h2> <div class="post-content"> <p>Hypercoordinated carbon has fascinated chemists since the development of the concept of the tetravalent carbon. The advent of superacids has opened up the world of hypercoordinated species and now a crystal structure of a hexacoordinated carbon has been reported for the C<sub>6</sub>(CH<sub>3</sub>)<sub>6</sub><sup>2+</sup> species <b>1</b>.<a href="#SixCoord"><sup>1</sup></a></p> <p align="center"><img src="/blog/wp-content/SixCoordImg.png"></p> <p>The molecule is prepared by first epoxidation of hexamethyl Dewar benzene, followed by reaction with Magic acid, and crystallized by the addition of HF. The crystal structure shows a pentamethylcyclopentadienyl base capped by a carbon with a methyl group. The x-ray structure is well reproduced by the B3LYP/def2-TZVP structure shown in Figure 1. (While this DFT method predicts a six-member isomer to be slightly lower in energy, MP2 does predict the cage as the lowest energy isomer.)</p> <table align="center" border="0" cellspacing="0" cellpadding="0"> <tr align="center"> <td> <p></p> <div class="jmol" id="SixCoord"> <a onclick="return false"><br> <img src="/blog/wp-content/SixCoord.jpg" onclick="insertJmol('SixCoord',300,300,'SixCoord.xyz')"></a> </div> <p><b>1</b></p> </td> </tr> </table> <p align="center"><b>Figure 1</b>. B3LYP/def2-TZVP optimized geometry of <b>1</b>.</p> <p>The Wiberg bond order for the bond between the capping carbon and each carbon of the five-member base is about 0.54, so the sum of the bond orders to the apical carbon is less than 4. The carbon is therefore not hypervalent, but it appears to truly be hypercoordinate. (A topological electron density analysis (AIM) study would have been interesting here.) NICS analysis indicates the cage formed by the apical carbon and the five-member ring expresses 3-D aromaticity. This can be thought of as coming from the C<sub>5</sub>(CH<sub>3</sub>)<sub>5</sub><sup>+</sup> fragment with its 4 electrons and the CCH<sub>3</sub><sup>+</sup> fragment with two electrons, providing 4<i>n </i>+ 2 = 6 electrons for the aromatic cage.</p> <h3>References</h3> <p><a name="SixCoord"></a></p> <p>1) Malischewski, M.; Seppelt, K., "Crystal Structure Determination of the Pentagonal-Pyramidal Hexamethylbenzene Dication C<sub>6</sub>(CH<sub>3</sub>)<sub>6</sub><sup>2+</sup>" <i>Angew. Chem. Int. Ed. </i><b>2017,</b> <i>56</i>, 368-370, DOI: <a href="http://dx.doi.org/10.1002/anie.201608795">10.1002/anie.201608795</a>.</p>  </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/aromaticity" rel="category tag">Aromaticity</a></span> <span class="user">Steven Bachrach</span> <span class="date">17 Jan 2017</span> <span class="comments"><a href="/blog/archives/3929#comments">2 Comments</a></span> </p> </div> <div class="box"> <h2><a href="/blog/archives/3923" rel="bookmark" title="Permanent Link: A Twisted Aromatic Makes for an Accessible Triplet State">A Twisted Aromatic Makes for an Accessible Triplet State</a></h2> <div class="post-content"> <p>Wentrup and co-workers examined the strained, non-planar aromatic <b>1</b>.<sup><a href="#wentrup1">1</a></sup></p> <p align="center"><img src="/blog/wp-content/wentrupImg1.png"></p> <p>The UKS-BP86-D3BJ/def2-TZVP optimized geometry of the singlet <b>1</b> is shown in Figure 1. The molecule is decidedly twisted, with an angle of about 52°. This large twist, weakening the π-bond between the two aromatic fragments, suggests that the triplet state of <b>1</b> might be easily accessible. The geometry of <sup>3</sup><b>1</b> is also shown in Figure 1, and the two aromatic portions are orthogonal.</p> <table align="center" border="0" cellspacing="0" cellpadding="4"> <tr align="center" valign="bottom"> <td> <p></p> <div class="jmol" id="wentrupSing"> <a onclick="return false"><br> <img src="/blog/wp-content/wentrupSing.jpg" onclick="insertJmol('wentrupSing',300,300,'wentrupSing.xyz')"></a> </div> <p><b><sup>1</sup>1</b></p> </td> <td> <p></p> <div class="jmol" id="wentrupTrip"> <a onclick="return false"><br> <img src="/blog/wp-content/wentrupTrip.jpg" onclick="insertJmol('wentrupTrip',300,300,'wentrupTrip.xyz')"></a> </div> <p><b><sup>3</sup>1</b></p> </td> </tr> </table> <p align="center"><b>Figure 1</b>. UKS-BP86-D3BJ/def2-TZVP optimized geometries of <b><sup>1</sup>1</b> and <b><sup>3</sup>1</b>.</p> <p>The proton and <sup>13</sup>C NMR studies of <b>1</b> show increasing paramagnetism, observed as line broadening, with increasing temperature. Confirming this is ESR which shows increasing signal with increasing temperature. The triplet state is clearly present. The experimental Δ<i>E</i><sub>ST</sub>=9.6 kcal mol<sup>-1</sup> and the computed singlet-triplet gap is 9.3 kcal mol<sup>-1</sup>. This is in excellent agreement, and much better than previous computations which predict a gap of 3.4 kcal mol<sup>-1</sup>, but omitted the D3 correction. This dispersion correction stabilizes the singlet state over the triplet state, as might be expected. (The triplet has the two aromatic components orthogonal and so they have minimal dispersion interactions, while the aromatic planes are much closer in the singlet state.)</p> <p>For comparison, the computed Δ<i>E</i><sub>ST</sub> of isomer <b>2</b> is much larger: 17.9 kcal mol<sup>-1</sup>. The energies of the triplet states of <b>1</b> and <b>2</b> are nearly identical. Both of these structures have orthogonal, non-interacting aromatic moieties. However, the energy of <b><sup>1</sup>2</b> with the twist angles of <b><sup>1</sup>1</b> is 8.2 kcal mol<sup>-1</sup> lower than that of <b><sup>1</sup>1</b>. This the twisting causes a significant strain to the singlet state, but not to the triplet, and that gives rise to its small singlet-triplet gap.</p> <p align="center"><img src="/blog/wp-content/wentrupImg2.png"></p> <h3>References</h3> <p><a name="wentrup1"></a></p> <p>1) Wentrup, C.; Regimbald-Krnel, M. J.; M眉ller, D.; Comba, P., "A Thermally Populated, Perpendicularly Twisted Alkene Triplet Diradical." <i>Angew. Chem. Int. Ed. </i><b>2016,</b> <i>55</i>, 14600-14605, DOI: <a href="http://dx.doi.org/10.1002/anie.201607415">10.1002/anie.201607415</a>.</p> <h3>InChIs</h3> <p><b>1</b>: InChI=1S/C42H24/c1-5-13-29-25(9-1)17-21-33-34-22-18-26-10-2-6-14-30(26)38(34)41(37(29)33)42-39-31-15-7-3-11-27(31)19-23-35(39)36-24-20-28-12-4-8-16-32(28)40(36)42/h1-24H<br>InChIKey=YEHKZURNXPRJHP-UHFFFAOYSA-N</p> <p><b>2</b>: InChI=1S/C42H24/c1-5-13-29-21-37-33(17-25(29)9-1)34-18-26-10-2-6-14-30(26)22-38(34)41(37)42-39-23-31-15-7-3-11-27(31)19-35(39)36-20-28-12-4-8-16-32(28)24-40(36)42/h1-24H<br>InChIKey=PKXAAFWZKNGAED-UHFFFAOYSA-N</p>  </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/aromaticity" rel="category tag">Aromaticity</a></span> <span class="user">Steven Bachrach</span> <span class="date">03 Jan 2017</span> <span class="comments"><a href="/blog/archives/3923#respond">No Comments</a></span> </p> </div> <p align="center"></p> </div> <div id="sidebar"> <ul> <li class="box"> <h2> Categories 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2015</a></li> <li><a href="/blog/archives/date/2014/12">December 2014</a></li> <li><a href="/blog/archives/date/2014/11">November 2014</a></li> <li><a href="/blog/archives/date/2014/10">October 2014</a></li> <li><a href="/blog/archives/date/2014/09">September 2014</a></li> <li><a href="/blog/archives/date/2014/08">August 2014</a></li> <li><a href="/blog/archives/date/2014/07">July 2014</a></li> <li><a href="/blog/archives/date/2014/06">June 2014</a></li> <li><a href="/blog/archives/date/2014/05">May 2014</a></li> <li><a href="/blog/archives/date/2014/04">April 2014</a></li> <li><a href="/blog/archives/date/2014/03">March 2014</a></li> <li><a href="/blog/archives/date/2014/02">February 2014</a></li> <li><a href="/blog/archives/date/2014/01">January 2014</a></li> <li><a href="/blog/archives/date/2013/12">December 2013</a></li> <li><a href="/blog/archives/date/2013/11">November 2013</a></li> <li><a href="/blog/archives/date/2013/10">October 2013</a></li> <li><a href="/blog/archives/date/2013/09">September 2013</a></li> <li><a href="/blog/archives/date/2013/08">August 2013</a></li> <li><a href="/blog/archives/date/2013/07">July 2013</a></li> <li><a href="/blog/archives/date/2013/06">June 2013</a></li> <li><a href="/blog/archives/date/2013/05">May 2013</a></li> <li><a href="/blog/archives/date/2013/04">April 2013</a></li> <li><a href="/blog/archives/date/2013/03">March 2013</a></li> <li><a href="/blog/archives/date/2013/02">February 2013</a></li> <li><a href="/blog/archives/date/2013/01">January 2013</a></li> <li><a href="/blog/archives/date/2012/12">December 2012</a></li> <li><a href="/blog/archives/date/2012/11">November 2012</a></li> <li><a href="/blog/archives/date/2012/10">October 2012</a></li> <li><a href="/blog/archives/date/2012/09">September 2012</a></li> <li><a href="/blog/archives/date/2012/08">August 2012</a></li> <li><a href="/blog/archives/date/2012/07">July 2012</a></li> <li><a href="/blog/archives/date/2012/06">June 2012</a></li> <li><a href="/blog/archives/date/2012/05">May 2012</a></li> <li><a href="/blog/archives/date/2012/04">April 2012</a></li> <li><a href="/blog/archives/date/2012/03">March 2012</a></li> <li><a href="/blog/archives/date/2012/02">February 2012</a></li> <li><a href="/blog/archives/date/2012/01">January 2012</a></li> <li><a href="/blog/archives/date/2011/12">December 2011</a></li> <li><a href="/blog/archives/date/2011/11">November 2011</a></li> <li><a href="/blog/archives/date/2011/10">October 2011</a></li> <li><a href="/blog/archives/date/2011/09">September 2011</a></li> <li><a href="/blog/archives/date/2011/08">August 2011</a></li> <li><a href="/blog/archives/date/2011/07">July 2011</a></li> <li><a href="/blog/archives/date/2011/06">June 2011</a></li> <li><a href="/blog/archives/date/2011/05">May 2011</a></li> <li><a href="/blog/archives/date/2011/04">April 2011</a></li> <li><a href="/blog/archives/date/2011/03">March 2011</a></li> <li><a href="/blog/archives/date/2011/02">February 2011</a></li> <li><a href="/blog/archives/date/2011/01">January 2011</a></li> <li><a href="/blog/archives/date/2010/12">December 2010</a></li> <li><a href="/blog/archives/date/2010/11">November 2010</a></li> <li><a href="/blog/archives/date/2010/10">October 2010</a></li> <li><a href="/blog/archives/date/2010/09">September 2010</a></li> <li><a href="/blog/archives/date/2010/08">August 2010</a></li> <li><a href="/blog/archives/date/2010/07">July 2010</a></li> <li><a href="/blog/archives/date/2010/06">June 2010</a></li> <li><a href="/blog/archives/date/2010/05">May 2010</a></li> <li><a href="/blog/archives/date/2010/04">April 2010</a></li> <li><a href="/blog/archives/date/2010/03">March 2010</a></li> <li><a href="/blog/archives/date/2010/02">February 2010</a></li> <li><a href="/blog/archives/date/2010/01">January 2010</a></li> <li><a href="/blog/archives/date/2009/12">December 2009</a></li> <li><a href="/blog/archives/date/2009/11">November 2009</a></li> <li><a href="/blog/archives/date/2009/10">October 2009</a></li> <li><a href="/blog/archives/date/2009/09">September 2009</a></li> <li><a href="/blog/archives/date/2009/08">August 2009</a></li> <li><a href="/blog/archives/date/2009/07">July 2009</a></li> <li><a href="/blog/archives/date/2009/06">June 2009</a></li> <li><a href="/blog/archives/date/2009/05">May 2009</a></li> <li><a href="/blog/archives/date/2009/04">April 2009</a></li> <li><a href="/blog/archives/date/2009/03">March 2009</a></li> <li><a href="/blog/archives/date/2009/02">February 2009</a></li> <li><a href="/blog/archives/date/2009/01">January 2009</a></li> <li><a href="/blog/archives/date/2008/12">December 2008</a></li> <li><a href="/blog/archives/date/2008/11">November 2008</a></li> <li><a href="/blog/archives/date/2008/10">October 2008</a></li> <li><a href="/blog/archives/date/2008/09">September 2008</a></li> <li><a href="/blog/archives/date/2008/08">August 2008</a></li> <li><a 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