{"id":21346,"date":"2019-10-03T10:04:07","date_gmt":"2019-10-03T09:04:07","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21346"},"modified":"2019-10-03T10:45:04","modified_gmt":"2019-10-03T09:45:04","slug":"bond-length-alternation-bla-in-large-conjugated-rings-an-update","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21346","title":{"rendered":"Bond length alternation (BLA) in large conjugated rings: an (anti-aromatic) update."},"content":{"rendered":"
\n

In the previous post<\/a>, I looked at a class of molecule known as hexaphyrins, inspecting bond length alternation (BLA) at the so-called meso<\/em> 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.
\n\"\"<\/a>Molecules in the bottom left of this diagram shows little or no bond length alternation. The right middle shows another cluster with more extreme (and unequal) bond length alternation. I have selected one molecule from this cluster, EGIJEK and it differs from EGIHUY in having four NH units in the ring, whereas the latter has only two.<\/p>\n

\"\"<\/a>

EGIJEK<\/p><\/div>

\"\"<\/a>

EGIHUY<\/p><\/div><\/p>\n

The effect this has is illustrated below. A pyrrole with an NH group contributes two\u00a0\u03c0-electrons to the conjugated periphery whereas a pyrrole with just an N contributes only one. Thus the four NH rings in EGIJEK contribute overall two more \u03c0-electrons to the periphery than EGIHUY with just two NH rings. This increases the \u03c0-electron count from 26 to 28, driving EGIJEK from a 4n+2 into a 4n \u03c0-electron count (n=7) and making it formally anti-aromatic. This in turn induces strong bond length alternation (as for example in cyclobutadiene).<\/p>\n

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

Here is a reprise of the bond length table shown in the previous post, but for\u00a0EGIJEK.<\/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
EGIJEK crystal, Ci<\/sub> symmetry, DOI: 10.5517\/ccrts2d<\/a><\/td>\n<\/tr>\n
1,43657<\/td>\n1.37034<\/td>\n0.06623<\/td>\n<\/tr>\n
1.35661<\/td>\n1.44895<\/td>\n0.09234<\/td>\n<\/tr>\n
1.42356<\/td>\n1.37287<\/td>\n0.05069<\/td>\n<\/tr>\n
B3LYP+GD3BJ\/Def2-SVPP (FAIR DOI: 10.14469\/hpc\/6194<\/a>)<\/td>\n<\/tr>\n
1.44019<\/td>\n1.38259<\/td>\n0.0576<\/td>\n<\/tr>\n
1.37732<\/td>\n1.44481<\/td>\n0.06749<\/td>\n<\/tr>\n
1.43261<\/td>\n1.38568<\/td>\n0.04693<\/td>\n<\/tr>\n
\u03c9B97XD\/Def2-SVPP (FAIR DOI: 10.14469\/hpc\/6194<\/a>\u00a0)<\/td>\n<\/tr>\n
1.44575<\/td>\n1.37537<\/td>\n0.07038<\/td>\n<\/tr>\n
1.36214<\/td>\n1.45508<\/td>\n0.09294<\/td>\n<\/tr>\n
1.44221<\/td>\n1.36958<\/td>\n0.07263<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Of the two functionals used in the calculations, the \u03c9B97XD form slightly over-estimates the BLA, with the B3LYP slightly under-estimating it. This seems to tally with the earlier observations<\/a> made for cyclo[n]carbons.<\/p>\n

Perhaps these sorts of molecules might form useful reality checks on calculating bond length alternations in large ring cyclic conjugated molecules.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

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. Molecules in the bottom left […]<\/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":[4],"tags":[],"ppma_author":[2661],"class_list":["post-21346","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nBond length alternation (BLA) in large conjugated rings: an (anti-aromatic) update. - 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=21346\" \/>\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 conjugated rings: an (anti-aromatic) update. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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. Molecules in the bottom left […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21346\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2019-10-03T09:04:07+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2019-10-03T09:45:04+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/09\/hexa-RT-1-1024x833.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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Bond length alternation (BLA) in large conjugated rings: an (anti-aromatic) update. - 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=21346","og_locale":"en_GB","og_type":"article","og_title":"Bond length alternation (BLA) in large conjugated rings: an (anti-aromatic) update. - Henry Rzepa's Blog","og_description":"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. 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Having found that different forms of quantum calculation seem to find this property particularly difficult to agree upon, not only for\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\/sq.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":30276,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=30276","url_meta":{"origin":21346,"position":1},"title":"Molecules of the year 2025: Cyclo[48]carbon and others – the onset of bond alternation and the Raman Activity Spectrum.","author":"Henry Rzepa","date":"December 29, 2025","format":false,"excerpt":"The annual \"Molecules of the Year\" selections are available for the year 2025. 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":21176,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21176","url_meta":{"origin":21346,"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":21225,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21225","url_meta":{"origin":21346,"position":3},"title":"Cyclo[6] and [10]carbon. The Kekul\u00e9 vibrations compared.","author":"Henry Rzepa","date":"September 3, 2019","format":false,"excerpt":"In the previous post, I looked at the so-called\u00a0Kekul\u00e9 vibration of cyclo[18]carbon using various quantum methods and basis sets. \u00a0Because some of these procedures can take a very long time, \u00a0I could not compare them using the same high-quality consistent atom basis set for the carbon (Def2-TZVPP). Here I try\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":21346,"position":4},"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":[]},{"id":21407,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21407","url_meta":{"origin":21346,"position":5},"title":"Does Kekulene have Kekul\u00e9 vibrational modes? Yes!","author":"Henry Rzepa","date":"October 19, 2019","format":false,"excerpt":"Increasingly, individual small molecules are having their structures imaged using STM, including cyclo[18]carbon that I recently discussed. The latest one receiving such treatment is Kekulene. As with cyclo[18]carbon, the point of interest was which of the two resonance structures shown below most closely resembled the measured structure. The one on\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\/10\/b3-1423-B2u-1024x575.gif?resize=350%2C200&ssl=1","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\/21346","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=21346"}],"version-history":[{"count":13,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21346\/revisions"}],"predecessor-version":[{"id":21362,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21346\/revisions\/21362"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21346"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21346"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21346"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21346"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}