{"id":21407,"date":"2019-10-19T09:06:10","date_gmt":"2019-10-19T08:06:10","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21407"},"modified":"2019-10-21T08:15:16","modified_gmt":"2019-10-21T07:15:16","slug":"does-kekulene-have-kekule-vibrational-modes-yes","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21407","title":{"rendered":"Does Kekulene have Kekul\u00e9 vibrational modes? Yes!"},"content":{"rendered":"
\n

Increasingly, individual small molecules are having their structures imaged<\/a> using STM, including cyclo[18]carbon<\/a> that I recently discussed. The latest one receiving such treatment is Kekulene.[1]<\/a><\/span>
\n\"\"<\/a><\/p>\n

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 the left has six cyclohexatriene motifs (red), also known as Clar rings (although I have argued they could also be called Armstrong rings<\/a>), with six largely isolated double bonds. These each follow the 4n+2\u00a0\u03c0-electron aromaticity rule (n=1). The structure on the right has instead two fully conjugated larger rings, the inner one blue following 4n+2, n=4 (18) and the outer one (magenta) following 4n+2, n=7 (30).<\/p>\n

Now, the STM result[1]<\/a><\/span> clearly came down in favour of the left hand structure, with a sextet of six-rings, rather than the larger annulenes implied by the right hand structure. A previously reported crystal structure[2]<\/a><\/span> came to a similar conclusion, and the species is shown<\/a> as fully planar. There is just one oddity about this structure. The distance between the inner six hydrogens is reported as 1.938\u00c5. In reality, it must be shorter, since the C-H bond lengths of these hydrogens are reported as 1.00\u00c5 whereas a more realistic value is ~1.09\u00c5. Applying this well-known correction means that the non-bonded H-H distance in Kekulene is actually closer to 1.83\u00c5, which is unusually close. Recollect a similar issue<\/a> arose in the imaging of purportedly planar tetraphenylporphrin, in which H…H distances as short as 0.8\u00c5 were implied in a published article.[3]<\/a><\/span><\/p>\n

Previously, I have shown that conjugated \u03c0-electron rings can exhibit Kekul\u00e9 vibrational modes for all these ring sizes<\/a>, and so the question arises as to the nature of any Kekul\u00e9 vibration in Kekulene itself. This vibration corresponds to a motion which creates two alternative cyclohexatriene structures (for benzene itself) from the symmetrical molecule. For benzene, this mode is real, ie<\/i> it takes energy to distort benzene into a cyclohexatriene. For larger annulenes, this vibration is imaginary and hence corresponds to a transition state between two bond alternating lower energy forms. So the Kekul\u00e9 vibration\u00a0in Kekulene should be distinctly different for the two structures shown above. I am using two different density functional methods, B3LYP+GD3BJ\/Def2-TZVPP and \u03c9B97XD\/Def2-TZVPP (FAIR DOI: 10.14469\/hpc\/6226<\/a>), which probably straddle<\/a> reality in terms of their propensity for bond length alternation (BLA) in larger annulene rings.<\/p>\n

The results show that a fully planar molecule with\u00a0D6h<\/sub> symmetry is actually a transition state in which three of these six inner hydrogen atoms move up and three down, giving a non-planar molecule with D3d<\/sub> symmetry and increasing the H…H separation.\u00a0However, both DFT methods also agree that there is just one<\/strong> Kekul\u00e9 vibration, which is real (\u03bd(A2g<\/sub>) 1389\/B3LYP or 1395\/\u03c9B97XD cm-1<\/sup>) and corresponds to the below.<\/p>\n

\"\"<\/a>

B3LYP<\/p><\/div>

\"\"<\/a>

wB97XD<\/p><\/div><\/p>\n

All six 6-membered Clar\/Armstrong rings are executing their own Kekul\u00e9 vibration, but in perfect synchrony with each other. There is almost no activity in the six passive double bonds. There is certainly no extended Kekul\u00e9 vibration similar to the one shown here<\/a> which involves the entire larger ring, whether in the inner or outer periphery.<\/p>\n

So these results match nicely with the initial crystal structure and the recent STM imaging one Curiously, no-one had ever mentioned the Kekul\u00e9 vibration in this species, and so this omission is rectified here.<\/p>\n

\n

Update:<\/b> Some variations on the theme above.<\/p>\n

    \n
  1. The inner ring of hydrogens is replaced by carbons
    \n    \"\"<\/a> This has the following Kekule modes, a B2u<\/sub> mode centered on just the inner six carbons (red, \u03bd 1423 cm-1<\/sup>)
    \n    \"\"<\/a>
    \nand a degenerate E2g<\/sub> mode (blue, \u03bd 1383 cm-1<\/sup>) for the six outer Clar rings.
    \n    \"\"<\/a><\/li>\n
  2. The inner ring is replaced by borons.
    \n
    \n\"\"<\/a><\/li>\n<\/ol>\n

    References<\/h2>\n
    1. I. Pozo, Z. Majzik, N. Pavli\u010dek, M. Melle-Franco, E. Guiti\u00e1n, D. Pe\u00f1a, L. Gross, and D. P\u00e9rez, \"Revisiting Kekulene: Synthesis and Single-Molecule Imaging\", Journal of the American Chemical Society<\/i>, vol. 141, pp. 15488-15493, 2019. https:\/\/doi.org\/10.1021\/jacs.9b07926<\/a>\n\n<\/li>\n
    2. H.A. Staab, F. Diederich, C. Krieger, and D. Schweitzer, \"Cycloarenes, a New Class of Aromatic Compounds, II. Molecular Structure and Spectroscopic Properties of Kekulene\", Chemische Berichte<\/i>, vol. 116, pp. 3504-3512, 1983. https:\/\/doi.org\/10.1002\/cber.19831161022<\/a>\n\n<\/li>\n
    3. J. Lee, K.T. Crampton, N. Tallarida, and V.A. Apkarian, \"Visualizing vibrational normal modes of a single molecule with atomically confined light\", Nature<\/i>, vol. 568, pp. 78-82, 2019. https:\/\/doi.org\/10.1038\/s41586-019-1059-9<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      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 the left has six cyclohexatriene […]<\/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-21407","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nDoes Kekulene have Kekul\u00e9 vibrational modes? Yes! - 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=21407\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Does Kekulene have Kekul\u00e9 vibrational modes? Yes! - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 the left has six cyclohexatriene […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21407\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2019-10-19T08:06:10+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2019-10-21T07:15:16+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/10\/kekulene.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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Does Kekulene have Kekul\u00e9 vibrational modes? 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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":30276,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=30276","url_meta":{"origin":21407,"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":21307,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21307","url_meta":{"origin":21407,"position":2},"title":"Bond length alternation (BLA) in large aromatic rings: an experimental reality check.","author":"Henry Rzepa","date":"September 30, 2019","format":false,"excerpt":"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\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":28773,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28773","url_meta":{"origin":21407,"position":3},"title":"Cyclo-S6 (Hexathiane) – anomeric effects again!","author":"Henry Rzepa","date":"June 1, 2025","format":false,"excerpt":"I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems\u00a0that I had described had an odd number of atoms and that I had not looked at any even numbered rings. Thus hexasulfur is a smaller (known) ring version of\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":21616,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21616","url_meta":{"origin":21407,"position":4},"title":"Molecules of the year – 2019: the incredible chloride cage.","author":"Henry Rzepa","date":"December 13, 2019","format":false,"excerpt":"Each year, C&E News runs a poll for their \"Molecule of the year\". I occasionally comment with some aspect of one of the molecules that catches my eye (I have already written about cyclo[18]carbon, another in the list). Here, it is the Incredible chloride cage, a cryptand-like container with an\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\/12\/cryptand-1024x847.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":18121,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18121","url_meta":{"origin":21407,"position":5},"title":"The \u03c0-\u03c0 stacking of aromatic rings: what is their closest parallel approach?","author":"Henry Rzepa","date":"April 13, 2017","format":false,"excerpt":"Layer stacking in structures such as graphite is well-studied. The separation between the \u03c0-\u03c0 planes\u00a0is\u00a0~3.35\u00c5, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7\u00c5). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen\u2026","rel":"","context":"In "crystal_structure_mining"","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\/04\/ring-distances-1024x709.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\/21407","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=21407"}],"version-history":[{"count":18,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21407\/revisions"}],"predecessor-version":[{"id":21434,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21407\/revisions\/21434"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21407"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21407"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21407"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21407"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}