{"id":24019,"date":"2021-09-04T13:17:10","date_gmt":"2021-09-04T12:17:10","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=24019"},"modified":"2021-09-04T17:57:58","modified_gmt":"2021-09-04T16:57:58","slug":"more-record-breakers-for-the-anomeric-effect-involving-c-n-bonds","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24019","title":{"rendered":"More record breakers for the anomeric effect involving C-N bonds."},"content":{"rendered":"
\n

An earlier post<\/a> investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom.<\/p>\n

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

A variation is to replace one oxygen by a nitrogen atom, as in N-C-O. Shown below is a scatter plot of the two distances to the common carbon atom derived from crystal structures.<\/p>\n

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

You can see some entries for which the C-O bond length is shorter than normal and the C-N distance very much longer than normal; an example of a highly asymmetric anomeric effect operating in just one direction rather than the two shown in the top diagram (red\/blue arrows).<\/p>\n

One example is LOFPON[1]<\/a><\/span> (DOI: 10.5517\/cc121rsn<\/a>) with bond lengths shown calculated at the \u03c9B97XD\/def2svpp level (Calculation DOI: 10.14469\/hpc\/8682<\/a>) and is rationalised by the nitrogen being a quaternary cation and hence an excellent leaving group which biases the electron flow towards it. Anomeric effects can be quantified using a technique known as NBO analysis, which uses perturbation theory to estimate the interaction energy between a donor orbital (the oxygen lone pair in this case) and an acceptor orbital (the C-N\u00a0\u03c3* unoccupied orbital). Populating the C-N\u00a0\u03c3* antibonding orbital causes the C-N length to increase and the interaction energy in this example is 36.4 kcal\/mol. This is around twice the normal value for anomeric effects and so is unusually large.<\/p>\n

\"\"<\/a>

LOFPON<\/p><\/div>\n

The other prominent example is NAWNUV (Data DOI: 10.5517\/cc93pkm<\/a>) where the bond length asymmetry is slightly larger and so is the perturbation energy (E2) is 41.0 kcal\/mol (\u03c9B97XD\/def2svpp calculation DOI: 10.14469\/hpc\/8378<\/a>).\u00a0<\/p>\n

\"\"<\/a>

NAWNUV<\/p><\/div>\n

In the opposite direction, NUQKAM[2]<\/a><\/span> is an example of a lengthened C-O bond and a shortened C-N bond, with the crystal structure (DOI: 10.5517\/ccv3ln5<\/a>)\u00a0shown below.<\/p>\n

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

In this instance, a \u03c9B97XD\/def2svpp calculation (Data DOI: 10.14469\/hpc\/8806<\/a>)\u00a0does not bear this structure out, with CN and CO bond lengths of 1.422 (vs 1.369) and\u00a01.434 (vs 1.529)\u00c5 and a final E(2) of 22.1 kcal\/mol (which is close to normal). This is an example of how mining the crystal structure can yield results that can be checked by a different (quantum computational) technique, which in this instance reveals a probable issue in the crystal structure refinement which is probably causing the apparently large anomeric effect in the crystal structure to manifest.<\/p>\n

Another\u00a0entry is ANUVUD[3]<\/a><\/span> with a crystal structure (data DOI: 10.5517\/ccdc.csd.cc24zxdg<\/a>)\u00a0shown below and CN and CO lengths of 1.391 and 1.559\u00c5, which in this case ARE reasonably replicated by calculation (1.402, 1.499). This effect is promoted by the good leaving group ability of the carboxylate anion and the antiperiplanar orientation of the nitrogen lone pair with respect to the C-O bond, E(2)=35.2 kcal\/mol (DOI: 10.14469\/hpc\/8807<\/a>)\"\"<\/a><\/p>\n

I end with FEHYOG, a relatively old structure[4]<\/a><\/span> showing a very long C-N distance (1.673\u00c5) but a normal associated C-O distance (1.423\u00c5). This rings an alarm bell. Indeed, the respective computed distances are 1.482 and 1.425\u00c5, a significant discrepancy (DOI: 10.14469\/hpc\/8769<\/a>). The NBO interaction energy is an umremarkable 12.5 kcal\/mol. \"\"<\/a><\/p>\n

Data mining of the crystal structure database has revealed a number of abnormally large bond length asymmetries around the N-C-O unit. Some of these are true record breakers, but two have been identified where calculations cannot reproduce the observed bond lengths. One might indeed ask whether a quantum computation of the structure might not be added to the curation checks made by the CCDC of their database. It might improve the quality of the data even further!<\/p>\n

References<\/h2>\n
  1. N. Mercadal, S.P. Day, A. Jarmyn, M.B. Pitak, S.J. Coles, C. Wilson, G.J. Rees, J.V. Hanna, and J.D. Wallis, \"<i>O<\/i>-<i>vs. N<\/i>-protonation of 1-dimethylaminonaphthalene-8-ketones: formation of a<i>peri<\/i>N\u2013C bond or a hydrogen bond to the pi-electron density of a carbonyl group\", CrystEngComm<\/i>, vol. 16, pp. 8363-8374, 2014. https:\/\/doi.org\/10.1039\/c4ce00981a<\/a>\n\n<\/li>\n
  2. A. Rivera, J.J. Rojas, J. R\u00edos-Motta, M. Du\u0161ek, and K. Fejfarov\u00e1, \"3,3\u2032-Ethylenebis(3,4-dihydro-6-chloro-2<i>H<\/i>-1,3-benzoxazine)\", Acta Crystallographica Section E Structure Reports Online<\/i>, vol. 66, pp. o1134-o1134, 2010. https:\/\/doi.org\/10.1107\/s1600536810014248<\/a>\n\n<\/li>\n
  3. Y. Wang, D. Sun, Y. Chen, J. Xu, Y. Xu, X. Yue, J. Jia, H. Li, and L. Chen, \"Alkaloids of Delphinium grandiflorum and their implication to H2O2-induced cardiomyocytes injury\", Bioorganic & Medicinal Chemistry<\/i>, vol. 37, pp. 116113, 2021. https:\/\/doi.org\/10.1016\/j.bmc.2021.116113<\/a>\n\n<\/li>\n
  4. N. Paillous, S.F. Forgues, J. Jaud, and J. Devillers, \"[2 + 2] Cycloaddition of two C\ue006N double bonds. First structural evidence for head-to-tail photodimerization in the 2-phenylbenzoxazole series\", J. Chem. Soc., Chem. Commun.<\/i>, pp. 578-579, 1987. https:\/\/doi.org\/10.1039\/c39870000578<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom. A variation is to replace one oxygen by a nitrogen atom, as in N-C-O. Shown below is a scatter plot of the two distances to the common carbon atom derived from crystal structures. You can see some entries […]<\/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":[1745,4],"tags":[],"ppma_author":[2661],"class_list":["post-24019","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry"],"yoast_head":"\nMore record breakers for the anomeric effect involving C-N bonds. - 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=24019\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"More record breakers for the anomeric effect involving C-N bonds. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom. 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You can see some entries […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24019\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2021-09-04T12:17:10+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-09-04T16:57:58+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/07\/anomeric.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":"More record breakers for the anomeric effect involving C-N bonds. - 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=24019","og_locale":"en_GB","og_type":"article","og_title":"More record breakers for the anomeric effect involving C-N bonds. - Henry Rzepa's Blog","og_description":"An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom. 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Here is another of these outliers (MUZZIS) which shows equally unusual properties. This is an oxyanion (counterion is\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\/2021\/07\/MUZZIS-1024x698.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":16696,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","url_meta":{"origin":24019,"position":1},"title":"A periodic table for anomeric centres, this time with quantified interactions.","author":"Henry Rzepa","date":"August 8, 2016","format":false,"excerpt":"The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I\u00a0quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:A two-coordinate atom across the series B-O and\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":16610,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610","url_meta":{"origin":24019,"position":2},"title":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens.","author":"Henry Rzepa","date":"July 8, 2016","format":false,"excerpt":"The previous post looked at anomeric effects set up on centres such as B, Si or P, and involving two oxygen groups attached to these atoms. Here I vary the attached groups to include either one or two nitrogen atoms..The\u00a0plot below shows aminols, C(NHR)(OR\"). A torsion along either the C-O\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":"aminol","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/07\/aminol-1-1024x773.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":26896,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26896","url_meta":{"origin":24019,"position":3},"title":"Detecting anomeric effects in tetrahedral carbon bearing four oxygen substituents.","author":"Henry Rzepa","date":"March 18, 2024","format":false,"excerpt":"I have written a few times about the so-called \"anomeric effect\", which relates to stereoelectronic interactions in molecules such as sugars bearing a tetrahedral carbon atom with at least two oxygen substituents. The effect can be detected when the two C-O bond lengths in such molecules are inspected, most obviously\u2026","rel":"","context":"In \"Interesting chemistry\"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=interesting-chemistry"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/03\/SILDOH.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\/2024\/03\/SILDOH.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/03\/SILDOH.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/03\/SILDOH.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/03\/SILDOH.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/03\/SILDOH.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":23973,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23973","url_meta":{"origin":24019,"position":4},"title":"Two record breakers for the anomeric effect; one real, the other not.","author":"Henry Rzepa","date":"July 1, 2021","format":false,"excerpt":"The classic anomeric effect operates across a carbon atom attached to oxygens. One (of the two) lone pairs on the oxygen can donate into the \u03c3* orbital of the C-O of the other oxygen (e.g. the red arrows) tending to weaken that bond whilst strengthening the donor oxygen C-O bond.\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\/2021\/07\/dist-vs-dist-1024x747.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":16601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16601","url_meta":{"origin":24019,"position":5},"title":"Anomeric effects at boron, silicon and phosphorus.","author":"Henry Rzepa","date":"July 1, 2016","format":false,"excerpt":"The anomeric effect occurs at 4-coordinate (sp3) carbon centres carrying two oxygen substituents and involves an alignment of a lone electron pair\u00a0on one oxygen with the adjacent C-O \u03c3*-bond of the other oxygen. Here I explore whether other centres can exhibit the phenomenon. I start with 4-coordinate boron, using the\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":"anomeric-bo-sq","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/anomeric-bo-sq-1024x644.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\/24019","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=24019"}],"version-history":[{"count":21,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/24019\/revisions"}],"predecessor-version":[{"id":24244,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/24019\/revisions\/24244"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24019"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24019"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24019"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=24019"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}