{"id":2469,"date":"2010-09-17T15:55:53","date_gmt":"2010-09-17T14:55:53","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469"},"modified":"2011-04-10T06:46:55","modified_gmt":"2011-04-10T06:46:55","slug":"solid-carbon-dioxide-hexacoordinate-carbon","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469","title":{"rendered":"Solid carbon dioxide: hexacoordinate carbon?"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"2469\">\n<p>Carbon dioxide is much in the news, not least because its atmospheric concentration is on the increase. How to sequester it and save the planet is a hot topic. Here I ponder its solid state structure, as a hint to its possible reactivity, and hence perhaps for clues as to how it might be captured. The structure was determined (DOI\u00a0<a href=\"http:\/\/dx.doi.org\/10.1103\/PhysRevB.65.104103\" target=\"_blank\">10.1103\/PhysRevB.65.104103<\/a>) as shown below.<\/p>\n<p><div id=\"attachment_2470\" style=\"width: 292px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2470\" class=\"size-full wp-image-2470\" title=\"CO2-solid\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('yellow');jmolApplet([600,600],'load wp-content\/uploads\/2010\/09\/SACBAA01.mol2;set measurementUnits Angstroms;connect (atomno=34) (atomno=41) PARTIAL;connect (atomno=41) (atomno=39) PARTIAL;connect (atomno=41) (atomno=5) PARTIAL;connect (atomno=45) (atomno=21) PARTIAL;connect (atomno=45) (atomno=26) PARTIAL;connect (atomno=41) (atomno=10) PARTIAL;measure 34 41;measure 39 41;measure 45 26;measure 21 45;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/CO2-solid.jpg\" alt=\"\" width=\"282\" height=\"298\" \/><p id=\"caption-attachment-2470\" class=\"wp-caption-text\">The structure of solid carbon dioxide. Click for 3D<\/p><\/div>The two nominal double bond distances are 1.33\u00c5, whilst a further four O&#8230;C contacts in the shape of a square complete the coordination (2.38\u00c5 each). All would probably agree that the central carbon is best described as hexa-coordinated. This is also a hot topic. For example, note the claim made recently to have created a hexa-coordinated carbon species by design (<em>Synthesis and Structure of a Hexacoordinate Carbon Compound<\/em>, DOI:\u00a0<a href=\"http:\/\/dx.doi.org\/10.1021\/ja710423d\" target=\"_blank\">10.1021\/ja710423d<\/a>) based on a motif derived from an allene:<\/p>\n<p><div id=\"attachment_2472\" style=\"width: 174px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2472\" class=\"size-full wp-image-2472\" title=\"hexacoord\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('yellow');jmolApplet([600,600],'load wp-content\/uploads\/2010\/09\/GOBMAM.cif;set measurementUnits Angstroms;connect (atomno=20) (atomno=40) PARTIAL;connect (atomno=21) (atomno=40) PARTIAL;measure 20 40;measure 21 40;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/hexacoord.jpg\" alt=\"\" width=\"164\" height=\"244\" \/><p id=\"caption-attachment-2472\" class=\"wp-caption-text\">Designed hexacoordinate carbon. Click for 3D<\/p><\/div>This claim was supported by an unusual measured property, the electron density \u03c1(r) and its Laplacian in the putative O&#8230;C region. These two properties are one of those (relatively rare) meetings between experiment and quantum mechanics, and their usefulness has been noted in <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=811\" target=\"_blank\">this blog<\/a> on <a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2251\" target=\"_blank\">previous occasions.<\/a> However, note that in this designed structure, the O&#8230;C distances are merely 2.65-2.7\u00c5, significantly longer than in solid carbon dioxide! So carbon dioxide, in a form many of us are familiar with (solid), can certainly be justified as being described as having a hexacoordinate carbon (although we might draw the line at describing it as having\u00a0<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878\" target=\"_blank\">hexavalent carbon<\/a>).<\/p>\n<p>If oxygen atoms can approach the carbon in CO<sub>2<\/sub> to within ~2.4\u00c5, an interesting question can be posed. How close can another carbon get to CO<sub>2<\/sub> without actually reacting and forming a new molecule? C-C bonds, even weak ones, are so much more interesting than C-O bonds! It would have to be a particularly nucleophilic carbon, of course. A search of the August 2010 version of the Cambridge structural database (CSD) reveals no really close approaches of another carbon to CO<sub>2<\/sub>. Only about 8 weak examples are found, and here the C-C distances are ~3.0-3.2\u00c5, with the O=C=O angle in the CO<sub>2<\/sub> never less than 170\u00b0. In this context, there is an intriguing and very recent report (which has not yet made it into the searchable CSD) of the structure of CO<sub>2<\/sub> trapped in a cavity next to what was claimed to be a molecule of 1,3-dimethyl cyclobutadiene, or CBD (see\u00a0<a href=\"http:\/\/dx.doi.org\/10.1126\/science.1188002\">10.1126\/science.1188002<\/a> and the discussion of this article in my\u00a0<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2355\" target=\"_blank\">earlier blog post<\/a>).\u00a0The focus in <a href=\"http:\/\/dx.doi.org\/10.1126\/science.1188002\" target=\"_blank\">that report<\/a> was on the &#8220;Mona Lisa of organic chemistry&#8221;, namely the CBD unit. One feels that the structure of the adjacent CO<sub>2<\/sub> was of lesser interest to the authors. According to a <a href=\"http:\/\/www-en.iemm.univ-montp2.fr\/\" target=\"_blank\">visual image of this system<\/a>, the CBD and CO<sub>2<\/sub> pair show quite an intimate approach <em>via<\/em> their carbon atoms (a ghostly C-C bond is clearly represented). This raises the interesting question of whether the description of this pair should be of two intimate but nevertheless separate and relatively unperturbed molecules not connected by a covalent bond (&#8220;<span style=\"font-size: 13.3333px;\"><a href=\"http:\/\/dx.doi.org\/10.1126\/science.1188002\" target=\"_blank\">more indicative of a strong van der Waals contact than of covalent bonding<\/a>&#8220;) <\/span><span style=\"font-size: 13.3333px;\"> or of a pair fully\u00a0bound by a covalent C-C bond between them?<\/span><\/p>\n<p>The issue of what is an interaction, and what is a bond continues to raise its often controversial head. And quantum theory continues to provide a multitude of interpretations as well.<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 2469 -->","protected":false},"excerpt":{"rendered":"<p>Carbon dioxide is much in the news, not least because its atmospheric concentration is on the increase. How to sequester it and save the planet is a hot topic. Here I ponder its solid state structure, as a hint to its possible reactivity, and hence perhaps for clues as to how it might be captured. [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_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}},"categories":[7,4],"tags":[292,296,144,289,285,291,290,295,282,294,293,2649,2648,286,297],"ppma_author":[2661],"class_list":["post-2469","post","type-post","status-publish","format-standard","hentry","category-hypervalency","category-interesting-chemistry","tag-13-dimethylcyclobutadiene","tag-borboiu","tag-cambridge","tag-carbon-dioxide","tag-cbd-and-co","tag-ccdc","tag-cds","tag-crystal-structure","tag-crystalline-calixarene-network","tag-guest","tag-host","tag-hypervalency","tag-interesting-chemistry","tag-often-controversial-head","tag-van-der-lee"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Solid carbon dioxide: hexacoordinate carbon? - 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=2469\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Solid carbon dioxide: hexacoordinate carbon? - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Carbon dioxide is much in the news, not least because its atmospheric concentration is on the increase. 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How to sequester it and save the planet is a hot topic. Here I ponder its solid state structure, as a hint to its possible reactivity, and hence perhaps for clues as to how it might be captured. [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2010-09-17T14:55:53+00:00","article_modified_time":"2011-04-10T06:46:55+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/CO2-solid.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Solid carbon dioxide: hexacoordinate carbon?","datePublished":"2010-09-17T14:55:53+00:00","dateModified":"2011-04-10T06:46:55+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469"},"wordCount":596,"commentCount":5,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/CO2-solid.jpg","keywords":["13-dimethylcyclobutadiene","Borboiu","Cambridge","carbon dioxide","CBD and CO","CCDC","CDS","crystal structure","crystalline calixarene network","guest","host","Hypervalency","Interesting chemistry","often controversial head","van der Lee"],"articleSection":["Hypervalency","Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2469","name":"Solid carbon dioxide: hexacoordinate carbon? 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Other journals (e.g.\u00a0Nature Chemistry ran the article as a research highlight (where the purpose\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.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/11\/cbd.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":936,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=936","url_meta":{"origin":2469,"position":1},"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":[]},{"id":2502,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2502","url_meta":{"origin":2469,"position":2},"title":"Secrets of a university admissions interviewer","author":"Henry Rzepa","date":"September 19, 2010","format":false,"excerpt":"Many university chemistry departments, and mine is no exception, like to invite applicants to our courses to show them around. Part of the activities on the day is an \"interview\" in which the candidate is given a chance to shine. Over the years, I have evolved questions about chemistry which\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.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/co2-trimer.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18277,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18277","url_meta":{"origin":2469,"position":3},"title":"How does carbon dioxide coordinate to a metal?","author":"Henry Rzepa","date":"May 6, 2017","format":false,"excerpt":"Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such. There are up to\u00a0five binding modes with one metal that one might envisage:\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/05\/078.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":2469,"position":4},"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":878,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=878","url_meta":{"origin":2469,"position":5},"title":"It&#8217;s Hexa-coordinate carbon Spock &#8211; but not as we know it!","author":"Henry Rzepa","date":"October 2, 2009","format":false,"excerpt":"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\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 HOMO orbital","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/C5-homo1.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\/2469","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=2469"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2469\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2469"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2469"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2469"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=2469"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}