{"id":878,"date":"2009-10-02T11:08:14","date_gmt":"2009-10-02T10:08:14","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878"},"modified":"2018-01-11T07:29:22","modified_gmt":"2018-01-11T07:29:22","slug":"its-hexa-coordinate-carbon-spock-but-not-as-we-know-it","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878","title":{"rendered":"It&#8217;s Hexa-coordinate carbon Spock &#8211; but not as we know it!"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"878\">\n<p>Science is about making connections. And these can often be made between the most unlikely concepts. Thus in the posts I have made about <strong>pentavalent carbon<\/strong>, one can identify a series of conceptual connections. The\u00a0first, by Matthias\u00a0Bickelhaupt and co, resulted in the suggestion of a possible <strong>frozen\u00a0S<sub>N<\/sub>2 transition state<\/strong>. They used astatine, and\u00a0this enabled a connection to be made between another good nucleophile\/nucleofuge,\u00a0cyclopentadienyl anion. This too seems to lead to a frozen\u00a0Sn2 transition state. The cyclopentadienyl theme then asks whether this anion can coordinate a much simpler unit, a C<sup>2+<\/sup> dication (rather than Bickelhaupt&#8217;s suggestion of a (NC)<sub>3<\/sub>C<sup>+<\/sup> cation\/radical) and indeed that complex is also frozen, again with 5-coordinate carbon, and this time with five equal C-C bonds. So here, the perhaps inevitable progression of ideas moves on to examining the properties of this complex, the outcome being a quite counter-intuitive suggestion which moves us into new territory.<\/p>\n<p>The journey starts with the previous observation that the HOMO of the carbyliumylidene cation, shown in the previous post, has prominent electron density along the five-fold symmetry axis of the molecule;<\/p>\n<div id=\"attachment_855\" style=\"width: 190px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-855\" class=\"size-full wp-image-855\" title=\"C5-homo\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2009\/09\/C5-40.jvxl;isosurface &quot;&quot; translucent;zoom 120;spin 3;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/C5-homo1.jpg\" alt=\"The HOMO orbital\" width=\"180\" height=\"221\" \/><p id=\"caption-attachment-855\" class=\"wp-caption-text\">The HOMO orbital. Click for 3D<\/p><\/div>\n<p>This suggests that the apical 5-coordinate carbon might actually be <strong>basic<\/strong>, and hence coordinate a proton to form a di-cation (below). So adding a proton results in the following stable (in the sense of having all positive force constants) structure, with apical C-C bond lengths of 1.7\u00c5 (compared to 1.8\u00c5 for the unprotonated system) and the bouncing castle\/trampoline mode of 875 cm<sup>-1<\/sup> (DOI: <a href=\"https:\/\/doi.org\/10.14469\/ch\/2410\">10.14469\/ch\/2410<\/a>) is likewise increased (for the pentamethyl derivative of the structure shown below). The apical C-H stretch has the highest value of all the CHs in the molecule, 3208 cm<sup>-1<\/sup>. The calculated proton affinity of the parent compound is 134.2 kcal\/mol. To put this into context, we can compare this value with a range of first and second proton affinities reported for carbon bases by\u00a0Frenking<span id=\"cite_ITEM-878-0\" name=\"citation\"><a href=\"#ITEM-878-0\">[1]<\/a><\/span>.\u00a0The highest second proton affinity there reported (ie protonation of an already positive system) is around\u00a0106 kcal\/mol, which is a good deal less than that found here! So we might conclude that our value must be a candidate for highest second proton affinity ever proposed for a carbon base.<\/p>\n<div id=\"attachment_879\" style=\"width: 252px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-879\" class=\"size-full wp-image-879\" title=\"C52+\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2009\/10\/c5-CH.cml; frame 1; zoom 100;connect (atomno=6) (atomno=4) PARTIAL;connect (atomno=6) (atomno=3) PARTIAL;connect (atomno=6) (atomno=2) PARTIAL;connect (atomno=6) (atomno=1) PARTIAL;connect (atomno=6) (atomno=5) PARTIAL;connect (atomno=4) (atomno=3) aromatic;connect (atomno=4) (atomno=5) aromatic;connect (atomno=1) (atomno=5) aromatic;connect (atomno=1) (atomno=2) aromatic;connect (atomno=2) (atomno=3) aromatic;measure 6 5;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/10\/C52+.jpg\" alt=\"Hexa-coordinate Carbon?\" width=\"242\" height=\"107\" \/><p id=\"caption-attachment-879\" class=\"wp-caption-text\">Hexa-coordinate Carbon?<\/p><\/div>\n<p>The value of \u03c1(r) for the AIM bond critical point located for each of the five apical C-C bonds is 0.156 au, again up from the value for the unprotonated species. As before, the Cp ring itself shows no ring critical point. An ELF analysis (below) shows five disynaptic basins in the C-C bond region, with the basin integrating to 0.75 electrons each. Together with the electrons in the\u00a0apical C-H bond,\u00a06.09 electrons are associated with basins surrounding this carbon atom. Both the\u00a0AIM and the\u00a0ELF concur in describing this carbon as not only hexa-coordinated, but hexavalent (although the bonds are not the conventional two-electron type, but perhaps more akin to a six-centre-four-electron interaction).<\/p>\n<div id=\"attachment_911\" style=\"width: 370px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-911\" class=\"size-full wp-image-911\" title=\"C5-elf\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2009\/10\/C5-CH-elf.mol; frame 1; zoom 100;spin 3;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/10\/C5-elf2.jpg\" alt=\"ELF Basins\" width=\"360\" height=\"350\" \/><p id=\"caption-attachment-911\" class=\"wp-caption-text\">ELF Basins. Click for 3D<\/p><\/div>\n<p>So I suggest that simple protonation of a highly basic cation has resulted in a six-coordinate carbon atom, which exhibits six strong bonds coordinated around it. I suppose it is inevitable again that one ends this post with the question whether this species too might one day be made.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-878-0\">R. Tonner, G. Heydenrych, and G. Frenking, \"First and Second Proton Affinities of Carbon Bases\", <i>ChemPhysChem<\/i>, vol. 9, pp. 1474-1481, 2008. <a href=\"https:\/\/doi.org\/10.1002\/cphc.200800208\">https:\/\/doi.org\/10.1002\/cphc.200800208<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 878 -->","protected":false},"excerpt":{"rendered":"<p>Science is about making connections. And these can often be made between the most unlikely concepts. Thus in the posts I have made about pentavalent carbon, one can identify a series of conceptual connections. The\u00a0first, by Matthias\u00a0Bickelhaupt and co, resulted in the suggestion of a possible frozen\u00a0SN2 transition state. They used astatine, and\u00a0this enabled a [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[7,4],"tags":[140,2649,2648,141],"ppma_author":[2661],"class_list":["post-878","post","type-post","status-publish","format-standard","hentry","category-hypervalency","category-interesting-chemistry","tag-chs","tag-hypervalency","tag-interesting-chemistry","tag-matthias-bickelhaupt"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>It&#039;s Hexa-coordinate carbon Spock - but not as we know it! - Henry Rzepa&#039;s Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"It&#039;s Hexa-coordinate carbon Spock - but not as we know it! - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Science is about making connections. And these can often be made between the most unlikely concepts. Thus in the posts I have made about pentavalent carbon, one can identify a series of conceptual connections. The\u00a0first, by Matthias\u00a0Bickelhaupt and co, resulted in the suggestion of a possible frozen\u00a0SN2 transition state. They used astatine, and\u00a0this enabled a [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2009-10-02T10:08:14+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2018-01-11T07:29:22+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/C5-homo1.jpg\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"It's Hexa-coordinate carbon Spock - but not as we know it! - Henry Rzepa&#039;s Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878","og_locale":"en_GB","og_type":"article","og_title":"It's Hexa-coordinate carbon Spock - but not as we know it! - Henry Rzepa&#039;s Blog","og_description":"Science is about making connections. And these can often be made between the most unlikely concepts. Thus in the posts I have made about pentavalent carbon, one can identify a series of conceptual connections. The\u00a0first, by Matthias\u00a0Bickelhaupt and co, resulted in the suggestion of a possible frozen\u00a0SN2 transition state. 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(Part 1).","author":"Henry Rzepa","date":"September 22, 2009","format":false,"excerpt":"The bimolecular nucleophilic substitution reaction at saturated carbon is an icon of organic chemistry, and is better known by its mechanistic label, SN2. It is normally a slow reaction, with half lives often measured in hours. This implies a significant barrier to reaction (~15-20 kcal\/mol) for the transition state, shown\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The Sn2 transition state","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/sn2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":845,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=845","url_meta":{"origin":878,"position":1},"title":"It&#8217;s penta-coordinate carbon Spock- but not as we know it!","author":"Henry Rzepa","date":"September 30, 2009","format":false,"excerpt":"In the previous two posts, I noted the recent suggestion of how a stable frozen SN2 transition state might be made. This is characterised by a central carbon with five coordinated ligands. The original suggestion included two astatine atoms as ligands (X=At), but in my post I suggested an alternative\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The Sn2 transition state","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/sn2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":811,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=811","url_meta":{"origin":878,"position":2},"title":"Capturing penta-coordinate carbon! (Part 2).","author":"Henry Rzepa","date":"September 23, 2009","format":false,"excerpt":"In this follow-up to the previous post, I will try to address the question what is the nature of the bonds in penta-coordinate carbon? This is a difficult question to answer with any precision, largely because our concept of a bond derives from trying to define what the properties of\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The Sn2 transition state","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/sn2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":7580,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7580","url_meta":{"origin":878,"position":3},"title":"The Sn2 reaction and the anomaly of carbon.","author":"Henry Rzepa","date":"September 6, 2012","format":false,"excerpt":"It was three years ago that I first blogged on the topic of the Sn2 reaction. Matthias Bickelhaupt had suggested that the Sn2 reaction involving displacement at a carbon atom was an anomaly; the true behaviour was in fact exhibited by the next element down in the series, silicon. The\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2-Na1.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17829,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17829","url_meta":{"origin":878,"position":4},"title":"First, hexacoordinate carbon &#8211; now pentacoordinate nitrogen?","author":"Henry Rzepa","date":"March 25, 2017","format":false,"excerpt":"A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure,\u00a0DOI:10.5517\/CCDC.CSD.CC1M71QM. Here is a\u00a0similar proposal for\u00a0penta-coordinate nitrogen. First, a search of the CSD (Cambridge structure database) for such\u00a0nitrogen.\u2026","rel":"","context":"In &quot;Bond slam&quot;","block_context":{"text":"Bond slam","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2237"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":936,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=936","url_meta":{"origin":878,"position":5},"title":"Full circle with carbon hypervalencies","author":"Henry Rzepa","date":"October 2, 2009","format":false,"excerpt":"The previous post talked about making links or connections. And part of the purpose for presenting this chemistry as a blog is to expose how these connections are made, or or less as it happens in real time (and\u00a0not the chronologically sanitized version of discovery that most research papers are).\u00a0So\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"C4-symmetric pentavalent carbon","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/10\/c4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/878","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=878"}],"version-history":[{"count":2,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/878\/revisions"}],"predecessor-version":[{"id":19346,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/878\/revisions\/19346"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=878"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=878"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=878"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=878"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}