{"id":14560,"date":"2015-09-13T07:09:46","date_gmt":"2015-09-13T06:09:46","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14560"},"modified":"2023-09-17T07:30:48","modified_gmt":"2023-09-17T06:30:48","slug":"deviations-from-planarity-of-trigonal-carbon-and-from-linearity-of-digonal-carbon","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560","title":{"rendered":"Deviations from planarity of trigonal carbon and from linearity of digonal carbon."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"14560\">\n<p>\n\t<a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14548\" target=\"_blank\" rel=\"noopener\">Previously<\/a>, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp<sup>3<\/sup>) carbon using crystal structures. Now it is the turn of digonal (sp<sup>1<\/sup>) and trigonal (sp<sup>2<\/sup>) carbons.&nbsp;\n<\/p>\n<p>\n\tFirstly, the digonal C&equiv;C case. Attached to each carbon of the C&equiv;C unit are two saturated carbon ligands; this to prevent conjugation from influencing our result.&nbsp;\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC-SQ.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tThe result of a search (R-factor &lt; 5%, no errors, no disorder) shows the hotspot at the expected ~180&deg;, but then a fascinating curve as the angle subtended at the digonal carbon angle decreases down to ~110&deg;, with the C&equiv;C bond length gradually increasing. This apparently non-linear behaviour would be interesting to replicate using quantum mechanics.<sup>&Dagger;<\/sup>\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC-angle.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tNext, the trigonal case. Again, the substituents are 4-coordinate carbons to prevent complicating conjugations.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/C=C-SQ.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tA plot of the C=C distance vs the C-C=C angle brings a surprise. There are four clusters centered at angles of ~132&deg;, 123&deg;, 110&deg; and 94&deg; (cyclobutenes) and a small cluster at ~150&deg;. The C=C distance stays constant at around 1.335&Aring; or shorter, a clear difference with the sp-case. There is perhaps a small outlier collection where the angle is ~108&deg; and the distance ~1.4&Aring;.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/C=C-angle.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tThis plots the dihedral angle subtended at one of the trigonal carbon atoms and measures how non-planar that atom is. There is again no real evidence that the C=C bond length changes as the trigonal centre becomes bent.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/C=C-dihed1.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tThis dihedral angle measures the twist about the C=C bond; up to about 30&deg; is tolerated, but again there is no clear indication of a systematic change in the C=C length.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/C=C-dihed2.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tThese analyses reveal general trends on bond lengths&nbsp;induced by distorting the normal coordination around trigonal and digonal carbon atoms. It is only the start of the story of course, since there are plenty of isolated outliers that really should be explored; some may be simply due to undetected crystallographic errors, whilst with others there may lurk interesting or even new chemical phenomena.&nbsp;\n<\/p>\n<hr \/>\n<p>\n\t<sup>&Dagger;<\/sup>Below, the crystal structure result (with the axes transposed) is compared to a closed shell single reference &omega;B97XD\/6-311+G(2df) calculation. Whilst the trend is&nbsp;replicated, it is not quantitative.&nbsp;This is probably because many of the crystal structures are perturbed by other effects, most probably by coordination of a metal and hence back-donation of &pi;-electrons into vacant metal orbitals. The CSD indexing of the structures however retains the C&equiv;C bond notation, even though the bond is no longer truly a triple one. This reinforces the observation I made in the previous post that when searching the CSD, one can stipulate a bond type to constrain the search. But that bond type may be purely nominal and bear little resemblance to the actual electronic structure of the species. There are other issues; &nbsp;the wave function was constrained to closed shell single determinant. At low angles, the calculation itself is probably not accurate (as can be seen from a kink in the plot, indicating instability).\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC-angle1.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"Scheme\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC.svg\" width=\"370\" \/>\n<\/p>\n<hr \/>\n<h4>Acknowledgments<\/h4>\n<p>This post has been cross-posted in PDF format at <a href=\"https:\/\/doi.org\/10.15200\/winn.145586.67623\" rel=\"noopener\" target=\"_blank\">Authorea<\/a>.<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 14560 -->","protected":false},"excerpt":{"rendered":"<p>Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons.&nbsp; Firstly, the digonal C&equiv;C case. Attached to each carbon of the C&equiv;C unit are two saturated carbon ligands; this to prevent conjugation from [&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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2,1745],"tags":[1548],"ppma_author":[2661],"class_list":["post-14560","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-chemical-phenomena"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Deviations from planarity of trigonal carbon and from linearity of digonal 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=14560\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Deviations from planarity of trigonal carbon and from linearity of digonal carbon. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons.&nbsp; Firstly, the digonal C&equiv;C case. Attached to each carbon of the C&equiv;C unit are two saturated carbon ligands; this to prevent conjugation from [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-09-13T06:09:46+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-17T06:30:48+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC-SQ.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":"Deviations from planarity of trigonal carbon and from linearity of digonal carbon. - 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=14560","og_locale":"en_GB","og_type":"article","og_title":"Deviations from planarity of trigonal carbon and from linearity of digonal carbon. - Henry Rzepa&#039;s Blog","og_description":"Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons.&nbsp; Firstly, the digonal C&equiv;C case. Attached to each carbon of the C&equiv;C unit are two saturated carbon ligands; this to prevent conjugation from [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2015-09-13T06:09:46+00:00","article_modified_time":"2023-09-17T06:30:48+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC-SQ.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=14560#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Deviations from planarity of trigonal carbon and from linearity of digonal carbon.","datePublished":"2015-09-13T06:09:46+00:00","dateModified":"2023-09-17T06:30:48+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560"},"wordCount":538,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC-SQ.jpg","keywords":["chemical phenomena"],"articleSection":["Chemical IT","crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560","name":"Deviations from planarity of trigonal carbon and from linearity of digonal carbon. - 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I had dealt with bond formation to a trigonal (sp2) carbon; now I add a digonal (sp) example (see an interesting literature variation).\u00a0 As before, I\u2026","rel":"","context":"In \"Baldwins rules\"","block_context":{"text":"Baldwins rules","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=baldwins-rules"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/06\/baldwin-dig.svg","width":350,"height":200},"classes":[]},{"id":23777,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23777","url_meta":{"origin":14560,"position":1},"title":"A suggestion for a molecule with a M\u2a78C quadruple bond with trigonal metal coordination.","author":"Henry Rzepa","date":"May 13, 2021","format":false,"excerpt":"The proposed identification of molecules with potential metal to carbon quadruple bonds, in which the metal exhibits trigonal bipyramidal coordination rather than the tetrahedral modes which have been proposed in the literature,, leads on to asking whether simple trigonal coordination at the metal can also sustain this theme? The rational\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":"","width":0,"height":0},"classes":[]},{"id":14548,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548","url_meta":{"origin":14560,"position":2},"title":"Deviations from tetrahedral four-coordinate carbon: a statistical exploration.","author":"Henry Rzepa","date":"September 6, 2015","format":false,"excerpt":"An article entitled \"Four Decades of the Chemistry of Planar Hypercoordinate Compounds\" was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":25581,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25581","url_meta":{"origin":14560,"position":3},"title":"Examples of inverted or hemispherical carbon?","author":"Henry Rzepa","date":"September 15, 2022","format":false,"excerpt":"In previously asking what the largest angle subtended at four-coordinate carbon might be, I noted that as the angle increases beyond 180\u00b0, the carbon becomes inverted, or hemispherical (all four ligands in one hemisphere). So what does a search for this situation reveal in the CSD? The query can be\u2026","rel":"","context":"With 2 comments","block_context":{"text":"With 2 comments","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25581#comments"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":845,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=845","url_meta":{"origin":14560,"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":8174,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8174","url_meta":{"origin":14560,"position":5},"title":"Mechanisms of carbon monoxide insertion reactions: A reality check on carbonylation of methyl manganese pentacarbonyl","author":"Henry Rzepa","date":"November 4, 2012","format":false,"excerpt":"When methyl manganese pentacarbonyl is treated with carbon monoxide in e.g. di-n-butyl ether, acetyl manganese pentacarbonyl is formed. This classic experiment conducted by Cotton (of quadruple bond fame) and Calderazzo in 1962 dates from an era when chemists conducted extensive kinetic analyses to back up any mechanistic speculations. Their suggested\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\/11\/CO%2Bethene.gif?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\/14560","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=14560"}],"version-history":[{"count":13,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14560\/revisions"}],"predecessor-version":[{"id":26508,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14560\/revisions\/26508"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14560"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14560"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14560"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14560"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}