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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 » 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, 2013</h2> <div class="box"> <h2><a href="/blog/archives/2570" rel="bookmark" title="Permanent Link: Displaying 3-D structures in the blog – a request for conversation">Displaying 3-D structures in the blog – a request for conversation</a></h2> <div class="post-content"> <p>With the recent disclosure of a major security hole in Java, I have been wondering if perhaps my continued use of the <i>Jmol</i> utility for displaying 3-D molecular structures makes sense. Perhaps it is time to consider alternatives. (Right now if you click on a molecule image in one of my blog posts and you are using Firefox, a big warning sign comes up first requiring the user to actively decide to invoke the <i>Jmol</i> viewer. Might this warning be enough to discourage some users?)</p> <p>In addition, the increasing use of mobile devices, which most often are not Java-enabled, suggests that moving to a new display option is warranted.</p> <p>So, I am asking the community to participate in a conversation about how we might best address this issue in the (near) future. Is a Javascript widget the way to go? If so, which current program are people happy with? Or should we move to an HTML5 approach? And if this is the way to go, what tools are people suggesting?</p> <p>If you want to see some fine examples of all three approaches (Java-based: <i>Jmol</i>, Javascipt-based: <i>Chemdoodle</i>, and HTML5-based: <i>GLMol</i>) I strongly encourage you to read Henry Rzepa’s recent brilliant article in <i>Journal of Cheminformatics</i> (DOI: <a href="http://dx.doi.org/10.1186/1758-2946-5-6">10.1186/1758-2946-5-6</a>). This is a fantastic article to compare the old-school publication technology (as presented in modern day PDF form) and new-school enabled technology (what Henry calls a <i>datument</i>). First download the pdf version and read it, and then access the HTML version; I guarantee you will be impressed by the difference in the experience.</p> <p>So, <b>please chime in on what molecular viewers I might adopt for this blog</b>, and perhaps we as a community might be able to encourage the use of and further the development of these enhanced publication technologies.</p>  </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/e-publishing" rel="category tag">E-publishing</a></span> <span class="user">Steven Bachrach</span> <span class="date">24 Jan 2013</span> <span class="comments"><a href="/blog/archives/2570#comments">3 Comments</a></span> </p> </div> <div class="box"> <h2><a href="/blog/archives/2516" rel="bookmark" title="Permanent Link: Covalently linked cycloparaphenylenes – onwards to nanotubes">Covalently linked cycloparaphenylenes – onwards to nanotubes</a></h2> <div class="post-content"> <p>Nanotubes are currently constructed in ways that offer little control of their size and chirality. The recent synthesis of cycloparaphenylenes (CPP) provides some hope that fully controlled synthesis of nanotubes might be possible in the near future. Jasti has now made an important step forward in preparing dimers of CPP such as <b>1</b>.<a href="#diCPP_1"><sup>1</sup></a></p> <table align="center" border="0" cellspacing="0" cellpadding="3"> <tr align="center"> <td> <p><img src="/blog/wp-content/diCPP1.png"><br><b>1</b></p> </td> <td> <p><img src="/blog/wp-content/diCPP2.png"><br><b>2</b></p> </td> </tr> </table> <p>They also performed B3LYP-D/6-31G(d,p) computations on <b>1</b> and the directly linked dimer <b>2</b>. The optimized geometries of these two compounds in their <i>cis</i> and <i>trans</i> conformations are shown in Figure 1. Interestingly, both compounds prefer to be in the <i>cis</i> conformation; <i>cis</i>–<b>1</b> is 10 kcal mol<sup>-1</sup> more stable than <i>trans</i>–<b>1</b> and <i>cis</i>–<b>2</b> is 30 kcal mol<sup>-1</sup> more stable than the <i>trans</i> isomer. While a true transition state interconnecting the two isomers was not located, a series of constrained optimizations to map out a reaction surface suggests that the<br> barrier for <b>1</b> is about 13 kcal mol<sup>-1</sup>. The authors supply an interesting movie of this pseudo-reaction path (<a href="http://pubs.acs.org/doi/suppl/10.1021/ja307373r/suppl_file/ja307373r_si_001.mpg">download the movie</a>).</p> <table align="center" border="0" cellspacing="0" cellpadding="3"> <tr align="center" valign="middle"> <td> <p></p> <div class="jmol" id="diCPPphCis"> <a onclick="return false"><br> <img src="/blog/wp-content/diCPPphCis.jpg" onclick="insertJmol('diCPPphCis',300,300,'diCPPphCis.xyz')"><br> </a> </div> <p><i>cis</i>–<b>1</b></p> </td> <td> <p></p> <div class="jmol" id="diCPPphTrans"> <a onclick="return false"><br> <img src="/blog/wp-content/diCPPphTrans.jpg" onclick="insertJmol('diCPPphTrans',300,300,'diCPPphTrans.xyz')"><br> </a> </div> <p><i>trans</i>–<b>1</b></p> </td> </tr> <tr align="center" valign="middle"> <td> <p></p> <div class="jmol" id="diCPPCis"> <a onclick="return false"><br> <img src="/blog/wp-content/diCPPCis.jpg" onclick="insertJmol('diCPPCis',300,300,'diCPPCis.xyz')"><br> </a> </div> <p><i>cis</i>–<b>2</b></p> </td> <td> <p></p> <div class="jmol" id="diCPPTrans"> <a onclick="return false"><br> <img src="/blog/wp-content/diCPPTrans.jpg" onclick="insertJmol('diCPPTrans',300,300,'diCPPTrans.xyz')"><br> </a> </div> <p><i>trans</i>–<b>2</b></p> </td> </tr> </table> <p align="center"><b>Figure 1</b>. B3LYP-D/6-31G(d,p) optimized geometries of the <i>cis</i> and <i>trans</i> conformers of <b>1</b> and <b>2</b>. (Be sure to click on these images to launch a 3-D viewer; these structures come to life in 3-D!)</p> <h3>References</h3> <p><a name="diCPP_1"></a></p> <p>(1) Xia, J.; Golder, M. R.; Foster, M. E.; Wong, B. M.; Jasti, R. "Synthesis, Characterization, and Computational Studies of Cycloparaphenylene Dimers," <i>J. Am. Chem. Soc.</i> <b>2012</b>, <i>134</i>, 19709-19715, DOI: <a href="http://dx.doi.org/10.1021/ja307373r">10.1021/ja307373r</a>.</p> <h3>InChIs</h3> <p><b>1</b>: InChI=1S/C106H82/c1-5-13-79-21-9-17-76-29-37-85(38-30-76)95-59-63-98(64-60-95)103-71-69-101(82(16-8-4)24-12-20-77-27-35-84(36-28-77)90-51-55-94(56-52-90)91-45-41-86(79)42-46-91)73-105(103)99-65-67-100(68-66-99)106-74-102-70-72-104(106)97-61-57-88(58-62-97)81(15-7-3)23-10-18-75-25-33-83(34-26-75)89-49-53-93(54-50-89)92-47-43-87(44-48-92)80(14-6-2)22-11-19-78-31-39-96(102)40-32-78/h5-16,21-74H,1-4,17-20H2/b21-9-,22-11-,23-10-,24-12-,79-13+,80-14+,81-15+,82-16+<br>InChIKey=WFVBBCVHFBTQRK-VPGVYKRGSA-N</p> <p><b>2</b>: InChI=1S/C100H78/c1-5-13-75-21-9-17-72-29-37-81(38-30-72)91-59-63-94(64-60-91)97-67-65-95(78(16-8-4)24-12-20-73-27-35-80(36-28-73)86-51-55-90(56-52-86)87-45-41-82(75)42-46-87)69-99(97)100-70-96-66-68-98(100)93-61-57-84(58-62-93)77(15-7-3)23-10-18-71-25-33-79(34-26-71)85-49-53-89(54-50-85)88-47-43-83(44-48-88)76(14-6-2)22-11-19-74-31-39-92(96)40-32-74/h5-16,21-70H,1-4,17-20H2/b21-9-,22-11-,23-10-,24-12-,75-13+,76-14+,77-15+,78-16+<br>InChIKey=HOODCSIDKUJYKE-XJQPCHFNSA-N</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">22 Jan 2013</span> <span class="comments"><a href="/blog/archives/2516#respond">No Comments</a></span> </p> </div> <div class="box"> <h2><a href="/blog/archives/2506" rel="bookmark" title="Permanent Link: A computationally inexpensive approach to correcting for BSSE">A computationally inexpensive approach to correcting for BSSE</a></h2> <div class="post-content"> <p>Basis set superposition error plagues all practical computations. This error results from the use of incomplete basis sets (thus pretty much <i>all</i> computations will suffer from this problem). The primary example of this error is in the formation of a supermolecule AB from the monomers A and B. Superposition occurs when in the computation of the supermolecule, basis functions centered on B are used to supplement the basis set of A, not to describe the bonding or interaction between the two monomers, but simply to better the description of the monomer A itself. Thus, BSSE always serves to increase the binding in the supermolecule. Recently, this concept has been extended to <i>intramolecular</i> BSSE, as discussed in these posts (<a href="/blog/archives/615">A</a> and <a href="/blog/archives/462">B</a>).</p> <p>The counterpoise correction proposed by Boys and Bernardi corrects for the superposition by computing the energy of each monomer using the basis sets centered on both monomers, often referred to as ghost orbitals because the functions are used but not the nuclei upon which they are centered. This can overcorrect for superposition but is the only widely utilized approach to treat the problem. A variation on this approach is what has been suggested for the intramolecular<br> BBSE problem.</p> <p>A major discouragement for wider use of counterpoise correction is its computational cost. Kruse and Grimme offer a semi-empirical approach that is extremely cost effective and appears to strongly mimic the traditional counterpoise correction.<a href="#gCP_1"><sup>1</sup></a></p> <p>They define the <i>geometric counterpoise</i> scheme (gCP) that provides an energy correction <i>E<sub>gCP</sub></i> that can be added onto the electronic energy. This term is defined as</p> <table align="center" border="0" cellspacing="2" cellpadding="10"> <tr align="center" valign="middle"> <td> <img src="/blog/wp-content/gCP1.png"> </td> <td> <p>Eq. (1)</p> </td> </tr> </table> <p>where σ is an empirically fitted scaling term. The atomic contributions are defined as</p> <table align="center" border="0" cellspacing="2" cellpadding="10"> <tr align="center" valign="middle"> <td> <p><img src="/blog/wp-content/gCP2.png"></p> </td> <td> <p>Eq. (2)</p> </td> </tr> </table> <p>where <i>e<sup>miss</sup></i> are the errors in the energy of an atom with a particular target basis set, relative to the energy with some large basis set:</p> <table align="center" border="0" cellspacing="2" cellpadding="10"> <tr align="center" valign="middle"> <td> <p><img src="/blog/wp-content/gCP3.png"></p> </td> <td> <p>Eq. (3)</p> </td> </tr> </table> <p>(On a technical matter, the atomic terms are computed in an electric field of 0.6a.u. in order to get some population into higher energy orbitals.) The <i>f<sub>dec</sub></i> term is a decay function that relates to the distance between the atoms (<i>R<sub>nm</sub></i>) and the overlap<br> (<i>S<sub>nm</sub></i>):</p> <table align="center" border="0" cellspacing="2" cellpadding="10"> <tr align="center" valign="middle"> <td> <p><img src="/blog/wp-content/gCP4.png"></p> </td> <td> <p>Eq. (4)</p> </td> </tr> </table> <p>where <i>N<sup>virt</sup></i> is the number of virtual orbitals on atom <i>m</i>, and α and β are fit parameters. Lastly, the overlap term comes from the integral of a single Slater orbital with coefficient</p> <table align="center" border="0" cellspacing="2" cellpadding="10"> <tr align="center" valign="middle"> <td> <p>ξ = η(ξ<sub>s</sub> + ξ<sub>p</sub>)/2</p> </td> <td> <p>Eq. (5)</p> </td> </tr> </table> <p>where ξ<sub>s</sub> and ξ<sub>p</sub> are optimized Slater exponents from extended Huckel theory, and η is the last parameter that needs to be fit.</p> <p>There are four parameters and these need to be fit for each specific combination of method (functional) and basis set. Kruse and Grimme provide parameters for a number of combinations, and suggest that the parameters devised for B3LYP are suitable for other functionals.</p> <p>So what is this all good for? They demonstrate that for a broad range of benchmark systems involving weak bonds, the that gCP corrected method coupled with the DFT-D3 dispersion correction provides excellent results, even with B3LYP/6-31G*! This allows one to potentially run a computation on very large systems, like proteins, where large basis sets, like TZP or QZP, would be impossible. In a follow-up paper,<a href="#gCP_2"><sup>2</sup></a> they show that the B3LYP/6-31G*-gCP-D3 computations of a few Diels-Alder reactions and computations of strain energies of fullerenes match up very well with computations performed at significantly higher levels. </p> <p>Once this gCP method and the D3 correction are fully integrated within popular QM programs, this combined methodology should get some serious attention. Even in the absence of this integration, these energy corrections can be obtained using the web service provided by Grimme at <a href="http://www.thch.uni-bonn.de/tc/gcpd3">http://www.thch.uni-bonn.de/tc/gcpd3</a>.</p> <h3>References</h3> <p><a name="gCP_1"></a></p> <p>(1) Kruse, H.; Grimme, S. "A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems," <i>J. Chem. Phys</i> <b>2012</b>, <i>136</i>, 154101-154116, DOI: <a href="http://dx.doi.org/10.1063/1.3700154">10.1063/1.3700154</a></p> <p><a name="gCP_2"></a></p> <p>(2) Kruse, H.; Goerigk, L.; Grimme, S. "Why the Standard B3LYP/6-31G* Model Chemistry Should Not Be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem," <i>J. Org. Chem.</i> <b>2012</b>, <i>77</i>, 10824-10834, DOI: <a href="http://dx.doi.org/10.1021/jo302156p">10.1021/jo302156p</a></p>  </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/bsse" rel="category tag">BSSE</a> &<a href="/blog/archives/category/authors/grimme" rel="category tag">Grimme</a></span> <span class="user">Steven Bachrach</span> <span class="date">15 Jan 2013</span> <span class="comments"><a href="/blog/archives/2506#respond">No Comments</a></span> </p> </div> <div class="box"> <h2><a href="/blog/archives/2537" rel="bookmark" title="Permanent Link: Benchmarked Dispersion corrected DFT and SM12">Benchmarked Dispersion corrected DFT and SM12</a></h2> <div class="post-content"> <p>This is a short post mainly to bring to the reader’s attention a couple of recent <i>JCTC</i> papers.</p> <p>The first is a benchmark study by Hujo and Grimme of the geometries produced by DFT computations that are corrected for dispersion.<a href="#HujoR1"><sup>1</sup></a> They use the S22 and S66 test sets that span a range of compounds expressing weak interactions. Of particular note is that the B3LYP-D3 method provided the best geometries, suggesting that this much (and justly) maligned functional can be significantly improved with just the simple D3 fix.</p> <p>The second paper entails the description of Truhlar and Cramer’s latest iteration on their solvation model, namely <i>SM12</i>.<a href="#JuhoR2"><sup>2</sup></a> The main change here is the use of Hirshfeld-based charges, which comprise their Charge Model 5 (CM5). The training set used to obtain the needed parameters is much larger than with previous versions and allows for treating a very broad set of solvents. Performance of the model is excellent.</p> <h3>References</h3> <p><a href="#HujoR1"></a></p> <p>(1) Hujo, W.; Grimme, S. "Performance of Non-Local and Atom-Pairwise Dispersion Corrections to DFT for Structural Parameters of Molecules with Noncovalent Interactions," <i>J. Chem. Theor. Comput.</i> <b>2013</b>, <i>9</i>, 308-315, DOI: <a href="http://dx.doi.org/10.1021/ct300813c">10.1021/ct300813c</a></p> <p><a href="#HujoR2"></a></p> <p>(2) Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. "Generalized Born Solvation Model SM12," <i>J. Chem. Theor. Comput.</i> <b>2013</b>, <i>9</i>, 609-620, DOI: <a href="http://dx.doi.org/10.1021/ct300900e">10.1021/ct300900e</a></p>  </div> <p class="bottom"> <span class="cat"><a href="/blog/archives/category/authors/cramer" rel="category tag">Cramer</a> &<a href="/blog/archives/category/qm-method/dft" rel="category tag">DFT</a> &<a href="/blog/archives/category/authors/grimme" rel="category tag">Grimme</a> &<a href="/blog/archives/category/solvation" rel="category tag">Solvation</a> &<a href="/blog/archives/category/authors/truhlar" rel="category tag">Truhlar</a></span> <span class="user">Steven Bachrach</span> <span class="date">14 Jan 2013</span> <span class="comments"><a href="/blog/archives/2537#respond">No Comments</a></span> </p> </div> <div class="box"> <h2><a href="/blog/archives/2478" rel="bookmark" title="Permanent Link: Long C-O bonds">Long C-O bonds</a></h2> <div class="post-content"> <p>I have written a number of posts discussing long C-C bonds (<a href="/blog/archives/2373">here</a> and <a href="/blog/archives/1883">here</a>). What about very long bonds between carbon and a heteroatom? Well, Mascal and co-workers<a href="#longCO1"><sup>1</sup></a> have computed the structures of some oxonium cations that express some very long C-O bonds. The champion, computed at MP2/6-31+G**, is the oxatriquinane <b>1</b>, whose C-O bond is predicted to be 1.602 Å! (It is rather disappointing that the optimized structures are not included in the supporting materials!) The long bond is attributed not to dispersion forces, as in the very long C-C bonds (see the other posts), but rather to σ(C-H) or σ(C-C) donation into the σ*(C-O) orbital.</p> <p align="center"><img src="/blog/wp-content/oxatriquinane.png"><br><b>1</b></p> <p>Inspired by these computations, they went ahead and synthesized <b>1</b> and some related species. They were able to get crystals of <b>1</b> as a (CHB<sub>11</sub>Cl<sub>11</sub>)<sup>–</sup> salt. The experimental C-O bond lengths for the x-ray crystal study are 1.591, 1.593, and 1.622 Å, confirming the computational prediction of long C-O bonds.</p> <p>As an aside, they also noted <i>many examples</i> of very long C-O distances within the Cambridge<br> Structural database that are erroneous – a cautionary note to anyone making use of this database to identify unusual structures.</p> <h3>References</h3> <p><a name="longCO1"></a></p> <p>(1) Gunbas, G.; Hafezi, N.; Sheppard, W. L.; Olmstead, M. M.; Stoyanova, I. V.; Tham, F. S.; Meyer, M. P.; Mascal, M. "Extreme oxatriquinanes and a record C–O bond length," <i>Nat. Chem.</i> <b>2012</b>, <i>4</i>, 1018-1023, DOI: <a href="http://dx.doi.org/10.1038/nchem.1502">10.1038/nchem.1502</a></p> <h3>InChIs</h3> <p><b>1</b>: InChI=1S/C21H39O/c1-16(2,3)19-10-12-20(17(4,5)6)14-15-21(13-11-19,22(19)20)18(7,8)9/h10-15H2,1-9H3/q+1/t19-,20+,21-<br>InChIKey=VTBHIDVLNISMTR-WKCHPHFGSA-N</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">07 Jan 2013</span> <span class="comments"><a href="/blog/archives/2478#comments">1 Comment</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 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href="/blog/archives/category/authors/schreiner">Schreiner</a> (29) </li> <li class="cat-item cat-item-6"> <a href="/blog/archives/category/authors/singleton">Singleton</a> (11) </li> <li class="cat-item cat-item-18"> <a href="/blog/archives/category/authors/truhlar">Truhlar</a> (8) </li> </ul> </li> <li class="cat-item cat-item-15"> <a href="/blog/archives/category/bond-dissociation-energy">Bond Dissociation Energy</a> (6) </li> <li class="cat-item cat-item-81"> <a href="/blog/archives/category/bsse">BSSE</a> (1) </li> <li class="cat-item cat-item-88"> <a href="/blog/archives/category/cyclophane">cyclophane</a> (0) </li> <li class="cat-item cat-item-4"> <a href="/blog/archives/category/dynamics">Dynamics</a> (35) </li> <li class="cat-item cat-item-57"> <a href="/blog/archives/category/e-publishing">E-publishing</a> (7) </li> <li class="cat-item cat-item-65"> <a href="/blog/archives/category/enzyme">Enzyme</a> (4) </li> <li class="cat-item cat-item-95"> <a href="/blog/archives/category/fep">FEP</a> (1) </li> <li class="cat-item cat-item-86"> <a href="/blog/archives/category/host-guest">host-guest</a> (6) </li> <li class="cat-item cat-item-84"> <a href="/blog/archives/category/hydrogen-bond">Hydrogen bond</a> (5) </li> <li class="cat-item cat-item-91"> <a href="/blog/archives/category/ion-pairs">Ion Pairs</a> (1) </li> <li class="cat-item cat-item-74"> <a href="/blog/archives/category/isotope-effects">Isotope Effects</a> (5) </li> <li class="cat-item cat-item-67"> <a href="/blog/archives/category/keto-enol-tautomerization">Keto-enol tautomerization</a> (3) </li> <li class="cat-item cat-item-54"> <a href="/blog/archives/category/molecules">Molecules</a> (100) <ul class="children"> <li class="cat-item cat-item-48"> <a href="/blog/archives/category/molecules/adamantane">adamantane</a> (3) </li> <li class="cat-item cat-item-26"> <a href="/blog/archives/category/molecules/amino-acids">amino acids</a> (13) </li> <li class="cat-item cat-item-19"> <a href="/blog/archives/category/molecules/annulenes">annulenes</a> (8) </li> <li class="cat-item cat-item-27"> <a href="/blog/archives/category/molecules/benzynes">benzynes</a> (4) </li> <li class="cat-item cat-item-46"> <a href="/blog/archives/category/molecules/biphenyl">biphenyl</a> (1) </li> <li class="cat-item cat-item-70"> <a href="/blog/archives/category/molecules/calixarenes">calixarenes</a> (1) </li> <li class="cat-item cat-item-33"> <a href="/blog/archives/category/molecules/carbenes">carbenes</a> (13) </li> <li class="cat-item cat-item-72"> <a href="/blog/archives/category/molecules/cyclobutadiene">cyclobutadiene</a> (4) </li> <li class="cat-item cat-item-62"> <a href="/blog/archives/category/molecules/dendralenes">dendralenes</a> (1) </li> <li class="cat-item cat-item-66"> <a href="/blog/archives/category/molecules/dewar-benzene">Dewar benzene</a> (1) </li> <li class="cat-item cat-item-39"> <a href="/blog/archives/category/molecules/diradicals">diradicals</a> (8) </li> <li class="cat-item cat-item-59"> <a href="/blog/archives/category/molecules/ephedrine">ephedrine</a> (1) </li> <li class="cat-item cat-item-37"> <a href="/blog/archives/category/molecules/ethyl-cation">ethyl cation</a> (2) </li> <li class="cat-item cat-item-90"> <a href="/blog/archives/category/molecules/fullerene">fullerene</a> (6) </li> <li class="cat-item cat-item-51"> <a href="/blog/archives/category/molecules/fulvalenes">fulvalenes</a> (1) </li> <li class="cat-item cat-item-21"> <a href="/blog/archives/category/molecules/hexacyclinol">hexacyclinol</a> (2) </li> <li class="cat-item cat-item-78"> <a href="/blog/archives/category/molecules/nanohoops">nanohoops</a> (4) </li> <li class="cat-item cat-item-41"> <a href="/blog/archives/category/molecules/non-classical">non-classical</a> (4) </li> <li class="cat-item cat-item-34"> <a href="/blog/archives/category/molecules/norbornyl-cation">norbornyl cation</a> (2) </li> <li class="cat-item cat-item-49"> <a href="/blog/archives/category/molecules/nucleic-acids">nucleic acids</a> (4) </li> <li class="cat-item cat-item-36"> <a href="/blog/archives/category/molecules/oximes">oximes</a> (1) </li> <li class="cat-item cat-item-75"> <a href="/blog/archives/category/molecules/phenyloxenium">phenyloxenium</a> (1) </li> <li class="cat-item cat-item-8"> <a href="/blog/archives/category/molecules/polycyclic-aromatics">polycyclic aromatics</a> (7) </li> <li class="cat-item cat-item-50"> <a href="/blog/archives/category/molecules/propellane">propellane</a> (2) </li> <li class="cat-item cat-item-79"> <a href="/blog/archives/category/molecules/stilbene">stilbene</a> (1) </li> <li class="cat-item cat-item-80"> <a href="/blog/archives/category/molecules/sugars">sugars</a> (5) </li> <li class="cat-item cat-item-85"> <a href="/blog/archives/category/molecules/terpenes">terpenes</a> (2) </li> <li class="cat-item cat-item-89"> <a href="/blog/archives/category/molecules/twistane">twistane</a> (1) </li> </ul> </li> <li class="cat-item cat-item-22"> <a href="/blog/archives/category/nmr">NMR</a> (40) </li> <li class="cat-item cat-item-31"> <a href="/blog/archives/category/optical-rotation">Optical Rotation</a> (16) </li> <li class="cat-item cat-item-28"> <a href="/blog/archives/category/qm-method">QM Method</a> (96) <ul class="children"> <li class="cat-item cat-item-20"> <a href="/blog/archives/category/qm-method/caspt2">CASPT2</a> (1) </li> <li class="cat-item cat-item-7"> <a href="/blog/archives/category/qm-method/dft">DFT</a> (71) </li> <li class="cat-item cat-item-45"> <a href="/blog/archives/category/qm-method/focal-point">focal point</a> (7) </li> <li class="cat-item cat-item-14"> <a href="/blog/archives/category/qm-method/g3">G3</a> (3) </li> <li class="cat-item cat-item-60"> <a href="/blog/archives/category/qm-method/mp">MP</a> (11) </li> </ul> </li> <li class="cat-item cat-item-56"> <a href="/blog/archives/category/reactions">Reactions</a> (83) <ul class="children"> <li class="cat-item cat-item-13"> <a href="/blog/archives/category/reactions/12-addition">1,2-addition</a> (1) </li> <li class="cat-item cat-item-35"> <a href="/blog/archives/category/reactions/aldol">aldol</a> (4) </li> <li class="cat-item cat-item-32"> <a href="/blog/archives/category/reactions/bergman-cyclization">Bergman cyclization</a> (6) </li> <li class="cat-item cat-item-44"> <a href="/blog/archives/category/reactions/claisen-rearrangement">Claisen rearrangement</a> (2) </li> <li class="cat-item cat-item-10"> <a href="/blog/archives/category/reactions/cope-rearrangement">Cope Rearrangement</a> (5) </li> <li class="cat-item cat-item-69"> <a href="/blog/archives/category/reactions/cycloadditions">cycloadditions</a> (12) </li> <li class="cat-item cat-item-23"> <a href="/blog/archives/category/reactions/diels-alder">Diels-Alder</a> (26) </li> <li class="cat-item cat-item-47"> <a href="/blog/archives/category/reactions/electrocyclization">electrocyclization</a> (11) </li> <li class="cat-item cat-item-76"> <a href="/blog/archives/category/reactions/electrophilic-aromatic-substitution">electrophilic aromatic substitution</a> (1) </li> <li class="cat-item cat-item-5"> <a href="/blog/archives/category/reactions/ene-reaction">ene reaction</a> (1) </li> <li class="cat-item cat-item-52"> <a href="/blog/archives/category/reactions/hajos-parrish-reaction">Hajos-Parrish Reaction</a> (1) </li> <li class="cat-item cat-item-61"> <a href="/blog/archives/category/reactions/mannich">Mannich</a> (2) </li> <li class="cat-item cat-item-64"> <a href="/blog/archives/category/reactions/michael-addition">Michael addition</a> (5) </li> <li 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">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" aria-current="page">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" src="https://i.creativecommons.org/l/by-nd/3.0/88x31.png"> </a> <br>This work is licensed under a <a rel="license" href="https://creativecommons.org/licenses/by-nd/3.0/">Creative Commons Attribution-No Derivative Works 3.0 Unported License</a>. </div>  <div class="clear"></div> </div>  <div id="footer"> <p>Copyright © 2021 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