{"id":21307,"date":"2019-09-30T08:28:15","date_gmt":"2019-09-30T07:28:15","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21307"},"modified":"2019-10-01T09:15:08","modified_gmt":"2019-10-01T08:15:08","slug":"bond-length-alternation-bla-in-large-aromatic-rings-an-experimental-reality-check","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21307","title":{"rendered":"Bond length alternation (BLA) in large aromatic rings: an experimental reality check."},"content":{"rendered":"
\n

The theme of the last three posts derives from the recently reported claimed experimental observation of bond length alternation (BLA) in cyclo[18]carbon, a ring of just 18 carbon atoms.[1]<\/a><\/span> Having found that different forms of quantum calculation seem to find this property particularly difficult to agree upon, not only for cyclocarbon but for twisted lemniscular annulenes (which contain CH rather than just C units), I thought it might be time to look at some more experimental data and my chosen system is a class called the hexaphyrins, of which there are a number of experimental crystal structures.<\/p>\n

The general form these molecules take is shown below. Here, QA can be N or S and the hashed bonds are defined as any type. T3 indicates an atom designated as having just three substituents. For each of the six meso carbons to which a non-metal (NM) is attached, a pair of C-C distances is specified as the search variable. These will define any bond length alternation.<\/p>\n

\"\"<\/a><\/p>\n

A search of the current crystal structure database specifies no errors and no disorder (see FAIR DOI: 10.1021\/ja801983d<\/a>). For any temperature, 64 hits are obtained. Specifying a temperature of < 95K and an R factor of <7.5% reduces the number to 18. The six pairs of distances are then processed for each molecule as follows;<\/p>\n

    \n
  1. The Abs()<\/strong> operator is chosen and the absolute value of the difference in values between each of the six pairs is calculated, using the minus<\/strong> operator.<\/li>\n
  2. Then using the Least()<\/strong> and Greatest()<\/strong> operators, the corresponding values for each of the six differences is calculated.<\/li>\n
  3. Finally, a Heat plot of the least vs<\/em> the greatest values is constructed for each of the molecules.<\/li>\n<\/ol>\n

    \"\"<\/a> The result is shown below for the first search\"\"<\/a><\/p>\n

    There are two main clusters.<\/p>\n

      \n
    1. The cluster with the hotspot (red) shows that the minimum and maximum BLA (bond length alternations) at any of the six meso carbon atoms is < 0.01\u00c5.<\/li>\n
    2. There is a second more diffuse cluster for which a greater minimum BLA at any meso atom of ~0.045\u00c5 and the maximum ~0.10\u00c5 are recorded.<\/li>\n
    3. The most diffuse cluster is where the minimum distance is 0.01\u00c5 but the maximum is again ~0.10\u00c5.<\/li>\n<\/ol>\n

      This result suggests that BLA may be sensitive to the nature of the substituents on the ring. Cluster 1 above, with the least BLA, may also arise because the crystal structure is actually the average of two BLA forms. We can reduce the temperature of the measurements to e.g.<\/em> < 95K to see the effect this might have on any dynamically averaging effect on the distances. A very similar distribution can be seen (below).<\/p>\n

      \"\"<\/a><\/p>\n

      Next, an equivalent search for octaphyrins. Although there are fewer examples, the same clustering is seen.<\/p>\n

      \"\"<\/a><\/p>\n

      The compound (code EGIHUY, a [26]phyrin, where 26 = 4n+2 = aromatic, DOI: 10.5517\/ccrts0b<\/a>[2]<\/a><\/span>) in the red hot spot in the top diagram, with the smallest\u00a0BLA was chosen for computation (FAIR data DOI: 10.14469\/hpc\/6179<\/a>). This has Ci<\/sub> symmetry and so only three pairs of distances need to be considered.<\/p>\n

      \"\"

      Click image for 3D model<\/p><\/div>\n

      The results show that both B3LYP and \u03c9B97XD DFT methods actually get pretty good geometries, reproducing the non-bond-alternating characteristics of this hexaphyrin. This in turn suggests that the absence of BLA may be real rather than a crystallographic averaging artefact.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
      Meso distances, \u00c5<\/th>\nabs(\u0394r)<\/th>\n<\/tr>\n
      EGIHUY crystal, Ci<\/sub> symmetry<\/td>\n<\/tr>\n
      1.39930<\/td>\n1.40168<\/td>\n0.00248<\/td>\n<\/tr>\n
      1.41029<\/td>\n1.39960<\/td>\n0.01069<\/td>\n<\/tr>\n
      1.40874<\/td>\n1.39902<\/td>\n0.00972<\/td>\n<\/tr>\n
      B3LYP+GD3BJ\/Def2-TZVPP<\/td>\n<\/tr>\n
      1.40842<\/td>\n1.40058<\/td>\n0.00784<\/td>\n<\/tr>\n
      1.39972<\/td>\n1.40963<\/td>\n0.00991<\/td>\n<\/tr>\n
      1.40848<\/td>\n1.40614<\/td>\n0.00234<\/td>\n<\/tr>\n
      \u03c9B97XD\/Def2-TZVPP<\/td>\n<\/tr>\n
      1.39636<\/td>\n1.40513<\/td>\n0.00877<\/td>\n<\/tr>\n
      1.40117<\/td>\n1.40680<\/td>\n0.00563<\/td>\n<\/tr>\n
      1.40730<\/td>\n1.39510<\/td>\n0.0122<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

      What has been achieved? Well, the crystal structures show that whilst some hexaphyrin molecules have no bond alternation, most in fact do. DFT calculations reproduce the lack of bond alternation in one molecule. The next step is to show whether they also reproduce those which do have BLA. The story is not ended yet!<\/p>\n

      References<\/h2>\n
      1. K. Kaiser, L.M. Scriven, F. Schulz, P. Gawel, L. Gross, and H.L. Anderson, \"An sp-hybridized molecular carbon allotrope, cyclo[18]carbon\", Science<\/i>, vol. 365, pp. 1299-1301, 2019. https:\/\/doi.org\/10.1126\/science.aay1914<\/a>\n\n<\/li>\n
      2. J. Sankar, S. Mori, S. Saito, H. Rath, M. Suzuki, Y. Inokuma, H. Shinokubo, K. Suk Kim, Z.S. Yoon, J. Shin, J.M. Lim, Y. Matsuzaki, O. Matsushita, A. Muranaka, N. Kobayashi, D. Kim, and A. Osuka, \"Unambiguous Identification of M\u00f6bius Aromaticity for<i>meso<\/i>-Aryl-Substituted [28]Hexaphyrins(1.1.1.1.1.1)\", Journal of the American Chemical Society<\/i>, vol. 130, pp. 13568-13579, 2008. https:\/\/doi.org\/10.1021\/ja801983d<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

        The theme of the last three posts derives from the recently reported claimed experimental observation of bond length alternation (BLA) in cyclo[18]carbon, a ring of just 18 carbon atoms. Having found that different forms of quantum calculation seem to find this property particularly difficult to agree upon, not only for cyclocarbon but for twisted lemniscular […]<\/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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[4],"tags":[],"ppma_author":[2661],"class_list":["post-21307","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nBond length alternation (BLA) in large aromatic rings: an experimental reality check. - Henry Rzepa'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=21307\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Bond length alternation (BLA) in large aromatic rings: an experimental reality check. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The theme of the last three posts derives from the recently reported claimed experimental observation of bond length alternation (BLA) in cyclo[18]carbon, a ring of just 18 carbon atoms. Having found that different forms of quantum calculation seem to find this property particularly difficult to agree upon, not only for cyclocarbon but for twisted lemniscular […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21307\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2019-09-30T07:28:15+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2019-10-01T08:15:08+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/09\/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":"Bond length alternation (BLA) in large aromatic rings: an experimental reality check. - Henry Rzepa'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=21307","og_locale":"en_GB","og_type":"article","og_title":"Bond length alternation (BLA) in large aromatic rings: an experimental reality check. - Henry Rzepa's Blog","og_description":"The theme of the last three posts derives from the recently reported claimed experimental observation of bond length alternation (BLA) in cyclo[18]carbon, a ring of just 18 carbon atoms. 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A theme was elemental allotropes and one such was carbon in the form of C48\u00a0stabilised by formation of a catenane C48.M3 (M = red ligand below) - it was not possible however to crystallise C48.M3. When \"unmasked\"\u2026","rel":"","context":"In "Interesting chemistry"","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":21346,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21346","url_meta":{"origin":21307,"position":1},"title":"Bond length alternation (BLA) in large conjugated rings: an (anti-aromatic) update.","author":"Henry Rzepa","date":"October 3, 2019","format":false,"excerpt":"In the previous post, I looked at a class of molecule known as hexaphyrins, inspecting bond length alternation (BLA) at the so-called meso position, the carbon atom joining two pyrrole rings. A search of the difference in bond lengths at this position had shown two significant clusters of crystal structures.\u2026","rel":"","context":"In "Interesting chemistry"","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\/2019\/09\/hexa-RT-1-1024x833.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":21176,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21176","url_meta":{"origin":21307,"position":2},"title":"Cyclo[18]carbon: The Kekul\u00e9 vibration calculated and hence a mystery!","author":"Henry Rzepa","date":"August 30, 2019","format":false,"excerpt":"I have discussed the vibration in benzene known as the Kekul\u00e9 mode in other posts, the first of which was all of ten years ago. It is a stretching mode that lengthens three of the bonds in benzene (a [6]-annulene) and shortens the other three, thus leading to a cyclohexatriene\u2026","rel":"","context":"In "Interesting chemistry"","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\/2019\/08\/C18.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":25581,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25581","url_meta":{"origin":21307,"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":28187,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28187","url_meta":{"origin":21307,"position":4},"title":"Molecules of the Year 2024: A crystal structure perspective on anti-Bredt olefins.","author":"Henry Rzepa","date":"January 8, 2025","format":false,"excerpt":"Each year C&E News publishes a list of candidates for the Molecule of the Year. For 2024 the list is (in order of votes cast for each) Mirror-image cyclodextrin Molecular shuttle in a box Rule-bending strained alkene First soluble promethium complex Single-electron carbon-carbon bond Hot MOF for capturing carbon I\u2026","rel":"","context":"In "Interesting chemistry"","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":21250,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21250","url_meta":{"origin":21307,"position":5},"title":"The Kekul\u00e9 vibration as a function of aromatic ring size. A different perspective using lemniscular rings.","author":"Henry Rzepa","date":"September 27, 2019","format":false,"excerpt":"In the previous posts, I tried to track down the onset of bond length alternation (BLA) as a function of ring size in aromatic cyclocarbons, finding the answer varied dramatically depending on the type of method used to calculate it. So here I change the system to an unusual kind\u2026","rel":"","context":"In "Interesting chemistry"","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":[]}],"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\/21307","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=21307"}],"version-history":[{"count":26,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21307\/revisions"}],"predecessor-version":[{"id":21340,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21307\/revisions\/21340"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21307"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21307"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21307"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21307"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}