{"id":14043,"date":"2015-05-30T13:16:09","date_gmt":"2015-05-30T12:16:09","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14043"},"modified":"2018-06-12T16:59:29","modified_gmt":"2018-06-12T15:59:29","slug":"discovering-chemical-concepts-from-crystal-structure-statistics-the-jahn-teller-effect","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043","title":{"rendered":"Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"14043\">\n<p>\n\tI am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. &nbsp;One colleague asked for a demonstration and suggested exploring the classical <a href=\"http:\/\/en.wikipedia.org\/wiki\/Jahn\u2013Teller_effect\" target=\"_blank\">Jahn-Teller effect<\/a>&nbsp;(thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example&nbsp;is illustrated&nbsp;by octahedral copper complexes which have a d<sup>9<\/sup> electronic configuration. The e<sub>g<\/sub> level shown below is occupied by three electrons and which can therefore distort in <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=2973\" target=\"_blank\">one of two ways<\/a> to eliminate the e<sub>g<\/sub> degeneracy by placing&nbsp;the odd&nbsp;electron into either a x<sup>2<\/sup>-y<sup>2<\/sup>&nbsp;or a z<sup>2<\/sup>&nbsp;orbital. Here I explore how this effect can be teased out of crystal structures.\n<\/p>\n<p>\n\t<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/JT.svg\"><img decoding=\"async\" alt=\"JT\" class=\"aligncenter size-full wp-image-14044\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/JT.svg\" width=\"300\" \/><\/a>\n<\/p>\n<p>\n\tThe search is set up with Cu specified as precisely 6-coordinate, and X=oxygen. The six X-Cu distances are defined as DIST1-DIST6. The R-factor is specified as &lt; 0.05 (no disorder, no errors). The problem now is how to plot what is in effect a six-dimensional set of data, from which we are exploring whether four of the distances are different from the other two, and whether those four are the longer or the shorter. This requires analysis beyond the capability (as far as I know) of the Conquest program, and so here I will show sets of plots showing just the relationship between any two distances at a time. Of the 15 possible combinations of two distances, only four are shown below.\n<\/p>\n<p>\n\tSome obvious patterns can already be spotted in the 400 or so compounds which satisfy the search criteria.\n<\/p>\n<ul>\n<li>\n\t\tThe largest clustering occurs at ~1.95&Aring;, with two clusters each of fewer hits at&nbsp;~2.5&Aring;. The <a href=\"http:\/\/en.wikipedia.org\/wiki\/Jahn\u2013Teller_effect\" target=\"_blank\">Wikipedia page<\/a> notes that for Cu(OH<sub>2<\/sub>)<sub>6<\/sub> the Jahn-Teller distortion favours four short bonds at ~1.95&Aring; and two long ones at ~2.38&Aring;, which agrees approximately with the positions and sizes of the centroids of these clusters.<sup>&dagger;<\/sup>\n\t<\/li>\n<li>\n\t\tPlots 1 and 2 show very little along the diagonals, where the two plotted distances have the same value. This probably means that one of the distances relates to an&nbsp;equatorial ligand and the other to an&nbsp;axial ligand.\n\t<\/li>\n<li>\n\t\tPlots 3 and 4 show a strong diagonal trend, and so these distances both relate to either axial or equatorial, but not one of each.\n\t<\/li>\n<li>\n\t\tAll four plots show a hot spot&nbsp;at ~1.95&Aring;, which hints that the Jahn-Teller distortion is four short bonds\/two long.\n\t<\/li>\n<li>\n\t\tPlot 4 also shows a green spot at ~2.5&Aring; which is a tantalising suggestion of examples of four long bonds\/two short.<sup>&Dagger;<\/sup>\n\t<\/li>\n<\/ul>\n<ol>\n<li>\n\t\t<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-12.jpg\"><img decoding=\"async\" alt=\"CuO-12\" class=\"aligncenter size-full wp-image-14050\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-12.jpg\" width=\"440\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-12.jpg 890w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-12-300x238.jpg 300w\" sizes=\"(max-width: 890px) 100vw, 890px\" \/><\/a>\n\t<\/li>\n<li>\n\t\t<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-34.jpg\"><img decoding=\"async\" alt=\"CuO-34\" class=\"aligncenter size-full wp-image-14049\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-34.jpg\" width=\"440\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-34.jpg 1016w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-34-300x231.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-34-900x692.jpg 900w\" sizes=\"(max-width: 1016px) 100vw, 1016px\" \/><\/a>\n\t<\/li>\n<li>\n\t\t<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-56.jpg\"><img decoding=\"async\" alt=\"CuO-56\" class=\"aligncenter size-full wp-image-14048\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-56.jpg\" width=\"440\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-56.jpg 1018w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-56-300x238.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-56-900x713.jpg 900w\" sizes=\"(max-width: 1018px) 100vw, 1018px\" \/><\/a>\n\t<\/li>\n<li>\n\t\t<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-13.jpg\"><img decoding=\"async\" alt=\"CuO-13\" class=\"aligncenter size-full wp-image-14047\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-13.jpg\" width=\"440\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-13.jpg 925w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-13-300x242.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/CuO-13-900x725.jpg 900w\" sizes=\"(max-width: 925px) 100vw, 925px\" \/><\/a>\n\t<\/li>\n<\/ol>\n<p>\n\tClearly this analysis can be followed up by a visual inspection of individual molecules in each cluster (as well as the outliers which appear to follow no pattern!), together with a more bespoke analysis of the six distances. Unfortunately, the spin state of the complexes cannot be quickly checked (are they all doublets?) since the database does not record these.&nbsp; But the basic search described above takes only a few minutes to do, and it is surprising at how quickly the Jahn-Teller effect can be statistically tested with real experimental data obtained for ~400 molecules. Of course, here I have only explored X=O but this can easily be extended to X=N or X=Cl, to other metals or to alternative coordination numbers such as <em>e.g.<\/em> 4 where the Jahn-Teller effect can also in principle operate.\n<\/p>\n<hr \/>\n<p>\n\t<sup>&Dagger;<\/sup> One genuine example of this type, also called compressed octahedral coordination, was reported for the species CuFAsF<sub>6<\/sub> and CsCuAlF<sub>6<\/sub><span id=\"cite_ITEM-14043-0\" name=\"citation\"><a href=\"#ITEM-14043-0\">[1]<\/a><\/span>\n<\/p>\n<hr \/>\n<p>\n\t<sup>&dagger;<\/sup> The measured geometry of Cu(H<sub>2<\/sub>O)<sub>6<\/sub> may in fact manifest with six equal Cu-O bond lengths due to the <i>dynamic Jahn-Teller effect<\/i>, because the kinetic barrier separating one Jahn-Teller distorted form and another (equivalent) isomer is small and hence averaged atom positions are measured which mask the effect. Thus the Jahn-Teller effects shown in the plots above may be under-estimated because of this dynamic masking. Reducing the temperature of the sample at which data was collected would reduce this dynamic effect. Indeed, Cu(D<sub>2<\/sub>O)<sub>6<\/sub> collected at 93K shows a very clear Jahn-Teller distortion<span id=\"cite_ITEM-14043-1\" name=\"citation\"><a href=\"#ITEM-14043-1\">[2]<\/a><\/span> with four short bonds ranging from 1.97-1.99&Aring; and two long bonds 2.37-2.39&Aring;.<span id=\"cite_ITEM-14043-2\" name=\"citation\"><a href=\"#ITEM-14043-2\">[3]<\/a><\/span> Another example measured at 89K with dimethyl formamide replacing water and coordinated <i>via<\/i> oxygen<span id=\"cite_ITEM-14043-3\" name=\"citation\"><a href=\"#ITEM-14043-3\">[4]<\/a><\/span> shows four short (1.97-1.98&Aring;) and two long (2.315&Aring;) bonds. This latter example is also noteworthy because this analysis is as yet unpublished in a journal, but the data itself has a DOI <i>via<\/i> which it can be acquired. A nice example of modern <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10972\" target=\"_blank\">research data management<\/a>!\n<\/p>\n<hr \/>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-14043-0\">Z. Mazej, I. Ar\u010don, P. Benki\u010d, A. Kodre, and A. Tressaud, \"Compressed Octahedral Coordination in Chain Compounds Containing Divalent Copper: Structure and Magnetic Properties of CuFAsF&lt;sub&gt;6&lt;\/sub&gt; and CsCuAlF&lt;sub&gt;6&lt;\/sub&gt;\", <i>Chemistry \u2013 A European Journal<\/i>, vol. 10, pp. 5052-5058, 2004. <a href=\"https:\/\/doi.org\/10.1002\/chem.200400397\">https:\/\/doi.org\/10.1002\/chem.200400397<\/a>\n\n<\/li>\n<li id=\"ITEM-14043-1\">W. Zhang, L. Chen, R. Xiong, T. Nakamura, and S.D. Huang, \"New Ferroelectrics Based on Divalent Metal Ion Alum\", <i>Journal of the American Chemical Society<\/i>, vol. 131, pp. 12544-12545, 2009. <a href=\"https:\/\/doi.org\/10.1021\/ja905399x\">https:\/\/doi.org\/10.1021\/ja905399x<\/a>\n\n<\/li>\n<li id=\"ITEM-14043-2\">Zhang, Wen., Chen, Li-Zhuang., Xiong, Ren-Gen., Nakamura, T.., and Huang, S.D.., \"CCDC 755150: Experimental Crystal Structure Determination\", 2010. <a href=\"https:\/\/doi.org\/10.5517\/cctbspl\">https:\/\/doi.org\/10.5517\/cctbspl<\/a>\n\n<\/li>\n<li id=\"ITEM-14043-3\">M.M. Olmstead, D.S. Marlin, and P.K. Mascharak, \"CCDC 1053817: Experimental Crystal Structure Determination\", 2015. <a href=\"https:\/\/doi.org\/10.5517\/cc14cl36\">https:\/\/doi.org\/10.5517\/cc14cl36<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 14043 -->","protected":false},"excerpt":{"rendered":"<p>I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. &nbsp;One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect&nbsp;(thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example&nbsp;is illustrated&nbsp;by octahedral copper complexes [&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":[976,1402,557,1395,1408,1409,1396,1401,1404,1406,1398,1397,356,1399,1403,1407,1405,1400],"ppma_author":[2661],"class_list":["post-14043","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-basic-search","tag-chemical-bond","tag-chemical-bonding","tag-chemistry","tag-classical-jahn-teller","tag-clear-jahn-teller","tag-coordination-chemistry","tag-coordination-complex","tag-copperii-nitrate","tag-dynamic-jahn-teller","tag-edward-teller","tag-inorganic-chemistry","tag-jahn-teller","tag-jahn-teller-effect","tag-metal-ions-in-aqueous-solution","tag-search-criteria","tag-technologyinternet","tag-transition-metals"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect - 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=14043\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. &nbsp;One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect&nbsp;(thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example&nbsp;is illustrated&nbsp;by octahedral copper complexes [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-05-30T12:16:09+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2018-06-12T15:59:29+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/JT.svg\" \/>\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=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect - 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=14043","og_locale":"en_GB","og_type":"article","og_title":"Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect - Henry Rzepa&#039;s Blog","og_description":"I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. &nbsp;One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect&nbsp;(thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example&nbsp;is illustrated&nbsp;by octahedral copper complexes [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2015-05-30T12:16:09+00:00","article_modified_time":"2018-06-12T15:59:29+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/JT.svg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect","datePublished":"2015-05-30T12:16:09+00:00","dateModified":"2018-06-12T15:59:29+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043"},"wordCount":775,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/05\/JT.svg","keywords":["basic search","Chemical bond","chemical bonding","Chemistry","classical Jahn-Teller","clear Jahn-Teller","Coordination chemistry","Coordination complex","Copper(II) nitrate","dynamic Jahn-Teller","Edward Teller","Inorganic chemistry","Jahn-Teller","Jahn\u2013Teller effect","Metal ions in aqueous solution","search criteria","Technology\/Internet","Transition metals"],"articleSection":["Chemical IT","crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14043","name":"Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect - 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The discussion about the norbornyl cation concentrated on whether this species existed in a single minimum symmetric energy well (the non-classical Winstein\/Olah proposal) or a double minimum well connected\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":20778,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20778","url_meta":{"origin":14043,"position":1},"title":"Imaging normal vibrational modes of a single molecule of CoTPP: a mystery about the nature of the imaged species.","author":"Henry Rzepa","date":"April 25, 2019","format":false,"excerpt":"Previously, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a \"flattened\" species on copper or gold surfaces for comparison with those recently imaged. The initial intent was to estimate the \"flattening\" energy. There are six electronic possibilities for this molecule on a metal surface. Respectively positively, or\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":15635,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15635","url_meta":{"origin":14043,"position":2},"title":"Bond stretch isomerism. Did this idea first surface 100 years ago?","author":"Henry Rzepa","date":"February 9, 2016","format":false,"excerpt":"The phenomenon of bond stretch isomerism, two isomers of a compound differing predominantly in just one bond length, is one of those chemical concepts that wax and occasionally\u00a0wane. Here I explore such isomerism for the elements Ge, Sn and Pb. In one earlier post, I noted a form of\u00a0bond stretch\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":"lewis1","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/02\/lewis1-1-1024x421.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":8570,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8570","url_meta":{"origin":14043,"position":3},"title":"The mechanism of the  Birch reduction. Sequel to benzene reduction.","author":"Henry Rzepa","date":"December 5, 2012","format":false,"excerpt":"I noted briefly in discussing why Birch reduction of benzene gives 1,4-cyclohexadiene (diagram below) that the geometry of the end-stage pentadienyl anion was distorted in the presence of the sodium cation to favour this product. This distortion actually has some pedagogic value, and so I elaborate this here. The starting\u2026","rel":"","context":"In \"antiaromaticity\"","block_context":{"text":"antiaromaticity","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=antiaromaticity"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/12\/benzene-22.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19207,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19207","url_meta":{"origin":14043,"position":4},"title":"Ammonide: an alkalide formed from ammonia and resembling an electride.","author":"Henry Rzepa","date":"December 17, 2017","format":false,"excerpt":"Alkalides are anionic alkali compounds containing e.g.\u00a0sodide (Na-), kalide (K-), rubidide (Rb-) or caeside (Cs-). Around 90 examples can be found in the Cambridge structure database (see DOI: 10.14469\/hpc\/3453\u00a0 for the search query and results). So what about the ammonium analogue, ammonide (NH4-)? A quick search of Scifinder drew a\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":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/12\/A1.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":485,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=485","url_meta":{"origin":14043,"position":5},"title":"Longer is stronger.","author":"Henry Rzepa","date":"June 6, 2009","format":false,"excerpt":"The iconic diagram below represents a cornerstone of organic chemistry. Generations of chemists have learnt early on in their studies of the subject that these two representations of where the electron pairs in benzene might be located (formally called electronic resonance or valence bond forms) each contribute ~50% to 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":"The Kekule structures of benzene.","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/06\/benzene.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\/14043","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=14043"}],"version-history":[{"count":22,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14043\/revisions"}],"predecessor-version":[{"id":19722,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14043\/revisions\/19722"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14043"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14043"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14043"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14043"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}