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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 » 2011 » April</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 April, 2011</h2> <div class="box"> <h2><a href="/blog/archives/1473" rel="bookmark" title="Permanent Link: indeno[1,2-b]fluorenes">indeno[1,2-b]fluorenes</a></h2> <div class="post-content"> <p>The search for ever more intriguing aromatic/antiaromatic species continues on – Haley has recently prepared the TIPS-protected indeno[1,2-b]fluorene <b>1</b>.<a href="#indenoFl1"> <sup>1</sup></a> The crystal structure was determined and analogue with the tri-<i>iso</i>-propylsilyl groups replaced with hydrogens (<b>2</b>) has been computed at B3LYP/6-31G(d,p). This optimized structure is shown in Figure 1. The core system has 20 π-electrons – suggesting perhaps an antiaromatic system. </p> <table border="0" cellspacing="0" cellpadding="3" align="center"> <tr align="center"> <td> <p><img src="/blog/wp-content/indFl.gif"><br><b>1</b></p> </td> </tr> <tr align="center"> <td> <p></p> <div class="jmol" id="indFl"> <a onclick="return false"><br> <img src="/blog/wp-content/indofluorene.jpg" onclick="insertJmol('indFl',325,325,'indofluorene.xyz')"><br> </a> </div> <p><b>2</b></p> </td> </tr> </table> <p align="center"><b>Figure 1</b>. B3LYP/6-31G(d,p) optimized geometry of <b>2</b>.</p> <p>The x-ray structure and computed structure are in close agreement in terms of distances. The terminal phenyl rings exhibit very little alternation. The C<sub>1</sub>-C<sub>2</sub> and C<sub>2</sub>-C<sub>3</sub> distances are long (1.444 and 1.457 Å, respectively) while the C<sub>1</sub>-C<sub>3A</sub> and C2-C<sub>4</sub> distances are short (1.379 and 1.396 Å, respectively.) This suggests a <i>para</i>-xylylene type structure for the central six-member ring. The NICS values of the terminal 6-member ring, the 5-member ring and the central 6-member ring are computed to be -7.12 (a reasonable phenyl value), 1.84, and 0.02. So the middle three rings possess no aromatic or antiaromatic character. Haley describes this structure as “a fully conjugated 20-π-electron hydrocarbon with fused <i>s-trans</i> 1,3-diene linkages across the top and bottom portions of the carbon skeleton”. </p> <h3>References</h3> <p><a name="indenoFl1"></a></p> <p>(1) Chase, D. T.; Rose, B. D.; McClintock, S. P.; Zakharov, L. N.; Haley, M. M., "Indeno[1,2-b]fluorenes: Fully Conjugated Antiaromatic Analogues of Acenes," <i>Angew. Chem. Int. Ed.</i>, <b>2011</b>, <i>50</i>, 1127-1130, DOI: <a href="http://dx.doi.org/10.1002/anie.201006312">10.1002/anie.201006312</a></p> <h3>InChIs</h3> <p><b>1</b>: InChI=1/C64H92Si4/c1-41(2)65(42(3)4,43(5)6)37-33-57-53-29-25-27-31-55(53)61-60(36-40-68(50(19)20,51(21)22)52(23)24)64-58(34-38-66(44(7)8,45(9)10)46(11)12)54-30-26-28-32-56(54)62(64)59(63(57)61)35-39-67(47(13)14,48(15)16)49(17)18/h25-32,41-52H,1-24H3<br>InChIKey=JIXLLIXVMPJPEE-UHFFFAOYAI</p> <p><b>2</b>: InChI=1/C28H12/c1-5-17-21-13-9-11-15-23(21)27-20(8-4)26-18(6-2)22-14-10-12-16-24(22)28(26)19(7-3)25(17)27/h1-4,9-16H<br>InChIKey=DOQPHDKEGVECBF-UHFFFAOYAY</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">20 Apr 2011</span> <span class="comments"><a href="/blog/archives/1473#respond">No Comments</a></span> </p> </div> <div class="box"> <h2><a href="/blog/archives/1448" rel="bookmark" title="Permanent Link: Describing hydrogen bonds with DFT">Describing hydrogen bonds with DFT</a></h2> <div class="post-content"> <p>Proper handling of hydrogen bonding using DFT remains a concern. Sherrill has reported a careful benchmark study using the potential energy curves for the six dimer combinations involving formic acid, formamide, and formamidine.<a href="#HBdft1"><sup>1</sup></a> Comparisons are made to the the CBS extrapolated limit CCSD(T) curve.</p> <p>As anticipated, B3LYP and related functionals do a poor job. Interestingly, PBE and PBE0 provide very nice curves. The meta-GGA functionals like M05-2x and M06-2x and functionals with dispersion corrections (like ωB97X-D) provide very good potential energy curves. It is clear that intermediate and long-range correlation and dispersion must be accounted for when handling hydrogen bonded systems. Proper selection of the functional is critical.</p> <h3>References</h3> <p><a name="HBdft1"></a></p> <p>(1) Thanthiriwatte, K. S.; Hohenstein, E. G.; Burns, L. A.; Sherrill, C. D., “Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions,” <i>J. Chem. Theory Comput.</i>, <b>2011</b>, <i>7</i>, 88-96, DOI: <a href="http://dx.doi.org/10.1021/ct100469b">10.1021/ct100469b</a>.</p>  </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/uncategorized" rel="category tag">Uncategorized</a></span> <span class="user">Steven Bachrach</span> <span class="date">05 Apr 2011</span> <span class="comments"><a href="/blog/archives/1448#respond">No Comments</a></span> </p> </div> <p align="center"></p> </div> <div id="sidebar"> <ul> <li class="box"> <h2> Categories </h2> <ul> <li class="cat-item cat-item-25"> <a href="/blog/archives/category/acidity">Acidity</a> (12) </li> <li class="cat-item cat-item-3"> <a href="/blog/archives/category/aromaticity">Aromaticity</a> (91) </li> <li class="cat-item cat-item-53"> <a href="/blog/archives/category/authors">Authors</a> (153) <ul class="children"> <li class="cat-item cat-item-42"> <a href="/blog/archives/category/authors/borden">Borden</a> (12) </li> <li class="cat-item cat-item-12"> 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