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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 » 2013 » November</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 November, 2013</h2> <div class="box"> <h2><a href="/blog/archives/2888" rel="bookmark" title="Permanent Link: Predicting reactive C-C bonds">Predicting reactive C-C bonds</a></h2> <div class="post-content"> <p>Can one identify a labile bond in a molecule without computing activation barriers? Markopoulos and Grunenberg suggest that examination of the bond length and its associated relaxed force constant might provide some guidance.<a href="#relaxed1"><sup>1</sup></a></p> <p>The relaxed force constant comes from identifying the force constant for some coordinate while allowing for other coordinates to relax. Badger’s rule relates the (normal) force constant to bond distance (<i>k</i> = a/(<i>r<sub>eq</sub></i> – <i>d</i>)<sup>3</sup>). For a series of 36 molecules, covering 71 C-C single bonds, Badger’s rule fits the data well, except for a set of molecules which undergo rapid Cope rearrangements (like bullvalene and semibullvalene). For these molecules, the relaxed force constants are much lower than Badger’s rule predicts, and indicates a weakened bond. This gives rise to their low activation barriers.</p> <p>Another example is provided with the highly strained polycyclic hydrocarbon <b>1</b>. This compound is predicted (B3LYP/6-31G(d)) to undergo a [1,2]-shift to give the carbene <b>2</b> (see Figure 1), and this is extremely exothermic: -105.7 kcal mol<sup>-1</sup>, reflecting the enormous strain of <b>1</b>. The barrier, through <b>TS1</b> (Figure 1), is only 6.7 kcal mol<sup>-1</sup>. This rearrangement was predicted by examining the relaxed force constants which identified a very weak bond, despite a short bond distance of 1.404 Å. It is unlikely that without this guidance, one would have predicted that this short bond is likely to rupture and produce this particular product.</p> <p align="center"><img src="/blog/wp-content/relaxedImage.png"></p> <table align="center" border="0" cellspacing="0" cellpadding="4"> <tr align="center" valign="bottom"> <td> <p></p> <div class="jmol" id="relaxed1"> <a onclick="return false"><br> <img src="/blog/wp-content/relaxed1.jpg" onclick="insertJmol('relaxed1',300,300,'relaxed1.xyz')"><br> </a> </div> <p><b>1</b></p> </td> <td> <p></p> <div class="jmol" id="relaxed2"> <a onclick="return false"><br> <img src="/blog/wp-content/relaxed2.jpg" onclick="insertJmol('relaxed2',300,300,'relaxed2.xyz')"><br> </a> </div> <p><b>2</b></p> </td> </tr> <tr align="center" valign="bottom"> <td colspan="2"> <p></p> <div class="jmol" id="relaxedTS1"> <a onclick="return false"><br> <img src="/blog/wp-content/relaxedTS1.jpg" onclick="insertJmol('relaxedTS1',300,300,'relaxedTS1.xyz')"><br> </a> </div> <p><b>TS1</b></p> </td> </tr> </table> <p align="center"><b>Figure 1</b>. B3LYP/6-31G(d) optimized structures of <b>1</b>, <b>2</b>, and <b>TS1</b>.</p> <h3>References</h3> <p><a name="relaxed1"></a></p> <p>(1) Markopoulos, G.; Grunenberg, J. "Predicting Kinetically Unstable C-C Bonds from the Ground-State Properties of a Molecule," <i>Angew. Chem. Int. Ed.</i> <b>2013</b>, <i>52</i>, 10648-10651, DOI: <a href="http://dx.doi.org/10.1002/anie.201303821">10.1002/anie.20130382</a>.</p> <h3>InChIs</h3> <p><b>1</b>: InChI=1S/C14H12/c1-2-8-11-5-3-9-7(1)10(9)4-6-12(8,11)14(8,11)13(7,9)10/h1-6H2<br> InChIKey=LNBZAENQMFDBJW-UHFFFAOYSA-N</p> <p><b>2</b>: InChI=1S/C14H12/c1-3-11-12-4-2-9-7-8(1,9)10(9)5-6-13(11,12)14(10,11)12/h1-6H2<br> InChIKey=UKVODHRLGFPZPT-UHFFFAOYSA-N</p>  </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/molecules/carbenes" rel="category tag">carbenes</a></span> <span class="user">Steven Bachrach</span> <span class="date">25 Nov 2013</span> <span class="comments"><a href="/blog/archives/2888#comments">3 Comments</a></span> </p> </div> <div class="box"> <h2><a href="/blog/archives/2915" rel="bookmark" title="Permanent Link: Tunneling in <i>t</i>-butylhydroxycarbene">Tunneling in <i>t</i>-butylhydroxycarbene</a></h2> <div class="post-content"> <p>Sorry I missed this paper from much earlier this year – it’s from a journal that’s not on my normal reading list. Anyways, here is another fantastic work from the Schreiner lab demonstrating the concept of tunneling control (see this <a href="/blog/archives/1660">post</a>).<a href="#tbutCarb1"><sup>1</sup></a> They prepare the <i>t</i>-butylhydroxycarbene <b>1</b> at low temperature to look for evidence of formation of possible products arising from a [1,2]-hydrogen shift (<b>2</b>), a [1,2]-methyl shift (<b>3</b>) or a [1,3]-CH insertion (<b>4</b>).</p> <p align="center"><img src="/blog/wp-content/tButCarbImg1.png"></p> <p>Schreiner performed CCSD(T)/cc-pVDZ optimizations of these compounds along with the transition states for the three migrations. The optimized geometries and relative energies are shown in Figure 1. The thermodynamic product is the aldehyde <b>2</b> while the kinetic product is the cyclopropane <b>4</b>, with a barrier of 23.8 kcal mol<sup>-1</sup> some 3.5 kcal mol<sup>-1</sup> lower than the barrier leading to <b>2</b>.</p> <table align="center" border="0" cellspacing="0" cellpadding="4"> <tr align="center"> <td rowspan="3"> <p></p> <div class="jmol" id="tButCarb1"> <a onclick="return false"><br> <img src="/blog/wp-content/tButCarb1.jpg" onclick="insertJmol('tButCarb1',200,200,'tButCarb1.xyz')"><br> </a> </div> <p><b>1</b><br>(0.0)</p> </td> <td> <p></p> <div class="jmol" id="tButCarbTS2"> <a onclick="return false"><br> <img src="/blog/wp-content/tButCarbTS2.jpg" onclick="insertJmol('tButCarbTS2',200,200,'tButCarbTS2.xyz')"><br> </a> </div> <p><b>TS2</b><br>(27.3)</p> </td> <td> <p></p> <div class="jmol" id="tButCarb2"> <a onclick="return false"><br> <img src="/blog/wp-content/tButCarb2.jpg" onclick="insertJmol('tButCarb2',200,200,'tButCarb2.xyz')"><br> </a> </div> <p><b>2</b><br>(-53.5)</p> </td> </tr> <tr align="center"> <td> <p></p> <div class="jmol" id="tButCarbTS3"> <a onclick="return false"><br> <img src="/blog/wp-content/tButCarbTS3.jpg" onclick="insertJmol('tButCarbTS3',200,200,'tButCarbTS3.xyz')"><br> </a> </div> <p><b>TS3</b><br>(31.0)</p> </td> <td> <p></p> <div class="jmol" id="tButCarb3"> <a onclick="return false"><br> <img src="/blog/wp-content/tButCarb3.jpg" onclick="insertJmol('tButCarb3',200,200,'tButCarb3.xyz')"><br> </a> </div> <p><b>3</b><br>(-41.0)</p> </td> </tr> <tr align="center"> <td> <p></p> <div class="jmol" id="tButCarbTS4"> <a onclick="return false"><br> <img src="/blog/wp-content/tButCarbTS4.jpg" onclick="insertJmol('tButCarbTS4',200,200,'tButCarbTS4.xyz')"><br> </a> </div> <p><b>TS4</b><br>(23.8)</p> </td> <td> <p></p> <div class="jmol" id="tButCarb4"> <a onclick="return false"><br> <img src="/blog/wp-content/tButCarb4.jpg" onclick="insertJmol('tButCarb4',200,200,'tButCarb4.xyz')"><br> </a> </div> <p><b>4</b><br>(-28.3)</p> </td> </tr> </table> <p align="center"><b>Figure 1</b>. CCSD(T)/cc-pVDZ optimized structures of <b>1-4</b> and the transition states for the three reaction. Relative energies in kcal mol<sup>-1</sup>.</p> <p>At low temperature (11 K), <b>1</b> is found to slowly convert into <b>2</b> with a half-life of 1.7 h. No other product is observed. Rates for the three reactions were also computed using the Wentzel-Kramers-Brillouin (WKB) method (which Schreiner and Allen have used in all of their previous studies). The predicted rate for the conversion of <b>1</b> into <b>2</b>, which takes place at 11 K solely through a tunneling process, is 0.4h, in quite reasonable agreement with experiment. The predicted rates for the other two potential reactions at 11 K are 10<sup>31</sup> and 10<sup>40</sup> years.</p> <p>This is clearly an example of tunneling control. The reaction occurs not across the lowest barrier, but <i>through the narrowest barrier</i>.</p> <h3>References</h3> <p><a name="tbutCarb1"></a></p> <p>(1) Ley, D.; Gerbig, D.; Schreiner, P. R. "Tunneling control of chemical reactions: C-H insertion <i>versus </i>H-tunneling in <i>tert</i>-butylhydroxycarbene," <i>Chem. Sci.</i> <b>2013</b>, <i>4</i>, 677-684, DOI: <a href="http://dx.doi.org/10.1039/C2SC21555A">10.1039/C2SC21555A</a>.</p> <h3>InChI</h3> <p><b>1</b>: InChI=1S/C5H10O/c1-5(2,3)4-6/h6H,1-3H3<br>InChIKey=ZGFKBRGJTPEEOC-UHFFFAOYSA-N</p> <p><b>2</b>: InChI=1S/C5H10O/c1-5(2,3)4-6/h4H,1-3H3<brinchikey> <p><b>3</b>: InChI=1S/C5H10O/c1-4(2)5(3)6/h6H,1-3H3<br>InChIKey=BZAZNULYLRVMSW-UHFFFAOYSA-N</p> <p><b>4</b>: InChI=1S/C5H10O/c1-5(2)3-4(5)6/h4,6H,3H2,1-2H3<br>InChIKey=MWWQKEGWQLBJBJ-UHFFFAOYSA-N</p>  </brinchikey></p> </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/authors/schreiner" rel="category tag">Schreiner</a> &<a href="/blog/archives/category/tunneling" rel="category tag">Tunneling</a></span> <span class="user">Steven Bachrach</span> <span class="date">11 Nov 2013</span> <span class="comments"><a href="/blog/archives/2915#respond">No Comments</a></span> </p> </div> <p align="center"></p> </div> <div id="sidebar"> <ul> <li class="box"> <h2> Categories </h2> 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class="cat-item cat-item-40"> <a href="/blog/archives/category/reactions/ozonolysis">ozonolysis</a> (1) </li> <li class="cat-item cat-item-43"> <a href="/blog/archives/category/reactions/proton-transfer">proton transfer</a> (1) </li> <li class="cat-item cat-item-38"> <a href="/blog/archives/category/reactions/pseudopericyclic">pseudopericyclic</a> (4) </li> <li class="cat-item cat-item-63"> <a href="/blog/archives/category/reactions/strecker">Strecker</a> (1) </li> <li class="cat-item cat-item-24"> <a href="/blog/archives/category/reactions/substitution">Substitution</a> (6) </li> <li class="cat-item cat-item-93"> <a href="/blog/archives/category/reactions/wittig">Wittig</a> (1) </li> </ul> </li> <li class="cat-item cat-item-87"> <a href="/blog/archives/category/second-edition">Second Edition</a> (3) </li> <li class="cat-item cat-item-11"> <a href="/blog/archives/category/solvation">Solvation</a> (17) </li> <li class="cat-item cat-item-77"> <a href="/blog/archives/category/stereochemistry">Stereochemistry</a> (2) </li> <li class="cat-item cat-item-68"> <a href="/blog/archives/category/stereoinduction">stereoinduction</a> (4) </li> <li class="cat-item cat-item-71"> <a href="/blog/archives/category/tunneling">Tunneling</a> (26) </li> <li class="cat-item cat-item-1"> <a href="/blog/archives/category/uncategorized">Uncategorized</a> (57) </li> <li class="cat-item cat-item-82"> <a href="/blog/archives/category/vibrational-frequencies">vibrational frequencies</a> (3) </li> </ul> </li> <li class="box"> <h2> Monthly </h2> <ul> <li><a href="/blog/archives/date/2019/06">June 2019</a></li> <li><a href="/blog/archives/date/2019/04">April 2019</a></li> <li><a href="/blog/archives/date/2019/03">March 2019</a></li> <li><a href="/blog/archives/date/2019/02">February 2019</a></li> <li><a href="/blog/archives/date/2019/01">January 2019</a></li> <li><a href="/blog/archives/date/2018/12">December 2018</a></li> <li><a href="/blog/archives/date/2018/11">November 2018</a></li> <li><a href="/blog/archives/date/2018/10">October 2018</a></li> <li><a href="/blog/archives/date/2018/09">September 2018</a></li> <li><a href="/blog/archives/date/2018/08">August 2018</a></li> <li><a href="/blog/archives/date/2018/07">July 2018</a></li> <li><a href="/blog/archives/date/2018/06">June 2018</a></li> <li><a href="/blog/archives/date/2018/05">May 2018</a></li> <li><a href="/blog/archives/date/2018/04">April 2018</a></li> <li><a href="/blog/archives/date/2018/03">March 2018</a></li> <li><a href="/blog/archives/date/2018/02">February 2018</a></li> <li><a href="/blog/archives/date/2018/01">January 2018</a></li> <li><a href="/blog/archives/date/2017/12">December 2017</a></li> <li><a href="/blog/archives/date/2017/11">November 2017</a></li> <li><a href="/blog/archives/date/2017/10">October 2017</a></li> <li><a href="/blog/archives/date/2017/09">September 2017</a></li> <li><a href="/blog/archives/date/2017/08">August 2017</a></li> <li><a href="/blog/archives/date/2017/07">July 2017</a></li> <li><a href="/blog/archives/date/2017/06">June 2017</a></li> <li><a href="/blog/archives/date/2017/05">May 2017</a></li> <li><a href="/blog/archives/date/2017/04">April 2017</a></li> <li><a href="/blog/archives/date/2017/03">March 2017</a></li> <li><a href="/blog/archives/date/2017/02">February 2017</a></li> <li><a href="/blog/archives/date/2017/01">January 2017</a></li> <li><a href="/blog/archives/date/2016/12">December 2016</a></li> <li><a href="/blog/archives/date/2016/11">November 2016</a></li> <li><a href="/blog/archives/date/2016/10">October 2016</a></li> <li><a href="/blog/archives/date/2016/09">September 2016</a></li> <li><a href="/blog/archives/date/2016/08">August 2016</a></li> <li><a href="/blog/archives/date/2016/07">July 2016</a></li> <li><a href="/blog/archives/date/2016/06">June 2016</a></li> <li><a href="/blog/archives/date/2016/05">May 2016</a></li> <li><a href="/blog/archives/date/2016/04">April 2016</a></li> <li><a href="/blog/archives/date/2016/03">March 2016</a></li> <li><a href="/blog/archives/date/2016/02">February 2016</a></li> <li><a href="/blog/archives/date/2016/01">January 2016</a></li> <li><a href="/blog/archives/date/2015/12">December 2015</a></li> <li><a href="/blog/archives/date/2015/11">November 2015</a></li> <li><a href="/blog/archives/date/2015/10">October 2015</a></li> <li><a href="/blog/archives/date/2015/09">September 2015</a></li> <li><a href="/blog/archives/date/2015/08">August 2015</a></li> <li><a href="/blog/archives/date/2015/07">July 2015</a></li> <li><a href="/blog/archives/date/2015/06">June 2015</a></li> <li><a href="/blog/archives/date/2015/05">May 2015</a></li> <li><a href="/blog/archives/date/2015/04">April 2015</a></li> <li><a href="/blog/archives/date/2015/03">March 2015</a></li> <li><a href="/blog/archives/date/2015/02">February 2015</a></li> <li><a href="/blog/archives/date/2015/01">January 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" aria-current="page">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 href="/blog/archives/date/2008/07">July 2008</a></li> <li><a href="/blog/archives/date/2008/06">June 2008</a></li> <li><a href="/blog/archives/date/2008/05">May 2008</a></li> <li><a href="/blog/archives/date/2008/04">April 2008</a></li> <li><a href="/blog/archives/date/2008/03">March 2008</a></li> <li><a href="/blog/archives/date/2008/02">February 2008</a></li> <li><a href="/blog/archives/date/2008/01">January 2008</a></li> <li><a href="/blog/archives/date/2007/12">December 2007</a></li> <li><a href="/blog/archives/date/2007/11">November 2007</a></li> <li><a href="/blog/archives/date/2007/10">October 2007</a></li> <li><a href="/blog/archives/date/2007/09">September 2007</a></li> <li><a href="/blog/archives/date/2007/08">August 2007</a></li> <li><a href="/blog/archives/date/2007/07">July 2007</a></li> </ul> </li> </ul> <a rel="license" href="https://creativecommons.org/licenses/by-nd/3.0/"> <img alt="Creative Commons License" style="border-width:0" 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