{"id":26009,"date":"2023-05-21T14:42:35","date_gmt":"2023-05-21T13:42:35","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=26009"},"modified":"2023-05-22T06:44:00","modified_gmt":"2023-05-22T05:44:00","slug":"tunable-aromaticity-an-unrecognized-new-aromatic-molecule","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26009","title":{"rendered":"Tunable aromaticity? An unrecognized new aromatic molecule?"},"content":{"rendered":"
\n

Some time ago in 2010, I showed a chemical problem<\/a> I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this. In that instance, it involved recognising that a cyclic molecule which appeared to have the cyclohexatriene benzene-aromatic pattern 1<\/strong> was in fact a trimer of carbon dioxide. Perhaps small amounts of this aromatic molecule exist in solutions of fizzy drinks? Analysing these patterns occupied about 10-20 minutes of an interview, and although you might think I was posing a difficult challenge, many students successfully rose to it! Now I revisit, but with a slightly better reality check on a related molecule 2 <\/strong>(cyanuric acid).<\/p>\n

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

As many as 58 examples of crystal structures of 1,3,5-triazinane-2,4,6-trione 2<\/strong> (cyanuric acid) are known, often with a co-adduct. Cyanuric acid is in effect a cyclic trimer of isocyanic acid rather than of carbon dioxide. These examples tend to be planar, with a mean C-N ring distance of ~1.37\u00c5 and a C-O distance of 1.22\u00c5.\u00a0<\/p>\n

\"\"<\/p>\n

Two outliers stand out, both from a very recently published article, being a co-adduct with melamine (1,3,5-triazine-2,4,6-triamine).[1]<\/a><\/span> QACSUI02<\/a> exhibits a shorter C-N distance of ~1.33\u00c5 but a longer C-O distances of 1.32\u00c5 and have a symmetrical patten of hydrogen bonds to the six receptors of the central unit. Could this correspond more closely to the cyclohexatriene resonance structures shown to the left of the diagram at the top? The first task is to see if these bond lengths can be replicated using calculation (often a useful procedure to check that the crystal structure is correct). For this purpose, the structure below was chosen as the starting point for various models, using an \u03c9B97XD\/Def2-TZVPP model.<\/p>\n

\"\"<\/p>\n\n\n\n\n\n\n\n\n\n\n
Model<\/th>\nC-N distance<\/th>\nC-O distance<\/th>\n<\/tr>\n
QACSUI02<\/a> (crystal structure)<\/td>\n1.331<\/strong><\/td>\n1.318<\/strong><\/td>\n<\/tr>\n
\u03c9B97XD\/Def2-TZVPP<\/a> as single layer<\/td>\n1.3678<\/td>\n1.2185<\/td>\n<\/tr>\n
\u03c9B97XD\/Def2-TZVPP<\/a> three layers<\/td>\n1.365<\/td>\n1.218<\/td>\n<\/tr>\n
\u03c9B97XD\/Def2-TZVPP<\/a> no H-bonds<\/td>\n1.3816<\/td>\n1.2002<\/td>\n<\/tr>\n
\n
\n<\/td>\n<\/tr>\n
XAKSOU<\/a> (crystal structure)<\/td>\n1.367<\/strong><\/td>\n1.208<\/strong><\/td>\n<\/tr>\n
\u03c9B97XD\/Def2-TZVPP<\/a>\u00a0<\/td>\n1.3670<\/td>\n1.2213<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

This creates a mystery. The calculated bond lengths show that whilst H-bonding to the central ring decreases the C-N length by 0.014\u00c5 and increases the C-O length by 0.017\u00c5, this effect is nowhere near large enough to match the apparent lengths in the crystal structure, where a C-N effect of ~0.037\u00c5 would be needed.<\/p>\n

Another system XAKSOU has been reported where discrete LiCl units replace the hydrogen the H-bonds formed to melamine above.[2]<\/a><\/span> A Li is coordinated to the carbonyl oxygen instead of a hydrogen bond, and a chloride anion from another molecule in the unit cell replaces the H-bond to nitrogen.<\/p>\n

\"\"<\/p>\n

In the computed model, an intramolecular Cl-H hydrogen bond is used as the model, resulting in similar C-N lengths as the crystal structure (one which does not match the lengths in the outlying crystal structure QACSUI02<\/a>)<\/p>\n

\"\"<\/p>\n

So the final question to ask is whether this latter structure is aromatic. NICS(0)\/(1) values of -2.8\/-1.1ppm<\/a> are computed, which suggests very little aromaticity (aromatic values would be -10 to -20 pm). So it does not seem as if aromaticity can be tuned into cyanuric acid 2 <\/strong>by polarising both the NH and CO units with ionic\/H-bond interactions so that the aromatic cyclohexatriene motif is better favoured over the 1,3,5-triazinane-2,4,6-trione non-aromatic resonance form. Are there any other examples where aromatically tunable molecules might be possible?<\/p>\n

References<\/h2>\n
  1. K. Song, H. Yang, B. Chen, X. Lin, Y. Liu, Y. Liu, H. Li, S. Zheng, and Z. Chen, \"The facile implementing ternary resistive memory in graphite-like melamine-cyanuric acid hydrogen-bonded organic framework with high ternary yield and environmental tolerance\", Applied Surface Science<\/i>, vol. 608, pp. 155161, 2023. https:\/\/doi.org\/10.1016\/j.apsusc.2022.155161<\/a>\n\n<\/li>\n
  2. O. Shemchuk, D. Braga, L. Maini, and F. Grepioni, \"Anhydrous ionic co-crystals of cyanuric acid with LiCl and NaCl\", CrystEngComm<\/i>, vol. 19, pp. 1366-1369, 2017. https:\/\/doi.org\/10.1039\/c7ce00037e<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Some time ago in 2010, I showed a chemical problem I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this. In that instance, it involved recognising that a cyclic molecule which appeared to have the cyclohexatriene benzene-aromatic pattern 1 was in […]<\/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_feature_clip_id":0,"_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":[1745],"tags":[],"ppma_author":[2661],"class_list":["post-26009","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining"],"yoast_head":"\nTunable aromaticity? An unrecognized new aromatic molecule? - 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=26009\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tunable aromaticity? An unrecognized new aromatic molecule? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Some time ago in 2010, I showed a chemical problem I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this. 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It has now been detected in the atmosphere of Titan, one of Saturn's moons and joins benzene, another aromatic molecule together with the protonated version of cyclopropenylidene, C3H3+ also\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":275,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=275","url_meta":{"origin":26009,"position":2},"title":"A molecule with an identity crisis: Aromatic or anti-aromatic?","author":"Henry Rzepa","date":"April 13, 2009","format":false,"excerpt":"In 1988, Wilke reported molecule 1 It was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned! The reason is that a\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":"A [24] annulene. Click on image for model.","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/gaytab.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24769,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24769","url_meta":{"origin":26009,"position":3},"title":"An unusually small (doubly) aromatic molecule: C4.","author":"Henry Rzepa","date":"March 15, 2022","format":false,"excerpt":"When you talk \u03c0-aromaticity, benzene is the first molecule that springs to mind.\u00a0But there are smaller molecules that can carry this property; cyclopropenylidene (five atoms) is the smallest in terms of atom count I could think of until now, apart that is from H3+ which is the smallest possible molecule\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":23410,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23410","url_meta":{"origin":26009,"position":4},"title":"The small-molecule antiviral compound Molnupiravir: an exploration of its tautomers.","author":"Henry Rzepa","date":"March 14, 2021","format":false,"excerpt":"For obvious reasons, anti-viral molecules are very much in the news at the moment. Thus Derek Lowe highlights Molnupiravir which is shown as a hydroxylamine, the representation originating from the Wikipedia page on the molecule. I like stereocentres more clearly identified using eg R\/S notation and so I went to\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\/2021\/03\/molnupiravir-1024x639.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":2502,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2502","url_meta":{"origin":26009,"position":5},"title":"Secrets of a university admissions interviewer","author":"Henry Rzepa","date":"September 19, 2010","format":false,"excerpt":"Many university chemistry departments, and mine is no exception, like to invite applicants to our courses to show them around. Part of the activities on the day is an \"interview\" in which the candidate is given a chance to shine. Over the years, I have evolved questions about chemistry which\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\/2010\/09\/co2-trimer.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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26009","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=26009"}],"version-history":[{"count":41,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26009\/revisions"}],"predecessor-version":[{"id":26085,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26009\/revisions\/26085"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26009"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26009"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26009"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=26009"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}