{"id":26962,"date":"2024-04-30T14:55:17","date_gmt":"2024-04-30T13:55:17","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=26962"},"modified":"2024-04-30T15:07:43","modified_gmt":"2024-04-30T14:07:43","slug":"detecting-anomeric-effects-in-tetrahedral-boron-bearing-four-oxygen-substituents","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26962","title":{"rendered":"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents."},"content":{"rendered":"
\n

In an earlier post, I discussed[1]<\/a><\/span> a phenomenon known as the “anomeric effect” exhibited by tetrahedral carbon compounds with four C-O bonds. Each oxygen itself bears two bonds and has two lone pairs, and either of these can align with one of three other C-O bonds to generate an anomeric effect. Here I change the central carbon to a boron to explore what happens, as indeed I promised earlier.<\/p>\n

One can identify candidates for such molecules by a constrained search of the CSD or the Cambridge structural database, as shown below.<\/p>\n

\"\"<\/p>\n

The four B-O distances for each compound matching the query are now subjected to further analysis, the greatest and least values are identified and the difference between them calculated.
\n\"\"<\/p>\n

The results are shown in the diagram below. Three outliers are identified for close inspection.
\n\"\"
\nEach of the three candidates is also subjected to a Gaussian calculation (MD15L\/Def2-TZVPP)[2]<\/a><\/span> (See DOI: 10.14469\/hpc\/14092<\/a>)<\/p>\n

    \n
  1. QIXREW[3]<\/a><\/span>. This molecule is overall neutral and for which \u0394rB-O<\/sub> = 0.193\u00c5 (MN15L\/Def2-TZVPP \u0394rB-O = <\/sub>0.175\u00c5). The Wiberg bond indices of longest and shortest B-O bonds are 0.486 and 0.698, \u0394 = 0.212\u00c5.This is significantly larger than the best example of the C-O series, for which the largest \u0394rC-O<\/sub> = 0.074\u00c5 and 0.137 for the Wiberg index.\"\"<\/li>\n
  2. XOVZOY[4]<\/a><\/span> is a tri-anion with intercalated\u00a0Ir3+<\/sup> counterion. \u0394rB-O<\/sub> = 0.347\u00c5. A calculation on the isolated tri-anion (with a continuum water field to help emulate the crystal environment) results in the maximum B-O bond length difference of only 0.004\u00c5, which is dramatically different from the crystal structure. This may be an example where the counter-ion is especially important for modelling structure, or it may be simply an anomalous refinement of the crystal structure. \"\"<\/li>\n
  3. KBDCTB, \u0394rB-O<\/sub> measured = 0.451\u00c5, Calculated 0.0314\u00c5.\"\"
    \nThis is another structure where all may not be what it seems. This again is an anionic structure and geometry optimisation of a single molecule results in a dramatic change in the internal hydrogen bonding of the species. In the crystal structure, the carboxylic acid groups all form intermolecular hydrogen bonds. Optimized as an isolated molecule, the former are no longer possible and a big conformational change occurs to allow all four carboxylic acid groups to instead form intramolecular H-bonds. In this conformation, all four B-O bonds are essentially the same length. So this might well be an example of a large change in anomeric effects due to changes in geometry induced by hydrogen bonding.<\/p>\n\n\n\n\n
    Intermolecular H-bonds<\/th>\nIntramolecular H-bonds<\/th>\n<\/tr>\n
    \"\"<\/td>\n\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ol>\n

    One lesson one always learns when comparing the lengths of bonds observed in crystal structures with those calculated using quantum mechanics is that they sometimes do not match well. These mis-matches can occur for various reasons; changes in hydrogen bonding, or the presence of unmodelled counterions or simply errors in the reported crystal structure. But we might suggest from this brief foray into B-O bonds that the anomeric effects found there may indeed be larger than those of their C-O counterparts.<\/p>\n

    References<\/h2>\n
    1. H. Rzepa, \"Detecting anomeric effects in tetrahedral carbon bearing four oxygen substituents.\", 2024. https:\/\/doi.org\/10.59350\/dfkt5-k2b20<\/a>\n\n<\/li>\n
    2. H. Rzepa, \"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents.\", 2024. https:\/\/doi.org\/10.14469\/hpc\/14092<\/a>\n\n<\/li>\n
    3. S.I. Kall\u00e4ne, T. Braun, B. Braun, and S. Mebs, \"Versatile reactivity of a rhodium(i) boryl complex towards ketones and imines\", Dalton Transactions<\/i>, vol. 43, pp. 6786, 2014. https:\/\/doi.org\/10.1039\/c4dt00080c<\/a>\n\n<\/li>\n
    4. H. Danjo, K. Hirata, S. Yoshigai, I. Azumaya, and K. Yamaguchi, \"Back to Back Twin Bowls of <i>D<\/i><sub>3<\/sub>-Symmetric Tris(spiroborate)s for Supramolecular Chain Structures\", Journal of the American Chemical Society<\/i>, vol. 131, pp. 1638-1639, 2009. https:\/\/doi.org\/10.1021\/ja8071435<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      In an earlier post, I discussed a phenomenon known as the “anomeric effect” exhibited by tetrahedral carbon compounds with four C-O bonds. Each oxygen itself bears two bonds and has two lone pairs, and either of these can align with one of three other C-O bonds to generate an anomeric effect. Here I change the […]<\/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":[],"tags":[],"ppma_author":[2661],"class_list":["post-26962","post","type-post","status-publish","format-standard","hentry"],"yoast_head":"\nDetecting anomeric effects in tetrahedral boron bearing four oxygen substituents. - 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=26962\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In an earlier post, I discussed a phenomenon known as the “anomeric effect” exhibited by tetrahedral carbon compounds with four C-O bonds. Each oxygen itself bears two bonds and has two lone pairs, and either of these can align with one of three other C-O bonds to generate an anomeric effect. Here I change the […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26962\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2024-04-30T13:55:17+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-04-30T14:07:43+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-2024-04-21-at-08.42.52.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=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents. - 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=26962","og_locale":"en_GB","og_type":"article","og_title":"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents. - Henry Rzepa's Blog","og_description":"In an earlier post, I discussed a phenomenon known as the “anomeric effect” exhibited by tetrahedral carbon compounds with four C-O bonds. Each oxygen itself bears two bonds and has two lone pairs, and either of these can align with one of three other C-O bonds to generate an anomeric effect. 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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":[]},{"id":26896,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26896","url_meta":{"origin":26962,"position":1},"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":14161,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161","url_meta":{"origin":26962,"position":2},"title":"The formation of tetrahedral intermediates.","author":"Henry Rzepa","date":"June 12, 2015","format":false,"excerpt":"In the preceding post, I discussed\u00a0the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly\u00a0pointed out\u00a0on this blog that his was a mixed-phase reaction, and that mechanistic comparison\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":24045,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24045","url_meta":{"origin":26962,"position":3},"title":"Another very large anomeric effect – with a twist.","author":"Henry Rzepa","date":"July 22, 2021","format":false,"excerpt":"In the earlier post on the topic of anomeric effects, I identified a number of outliers associated with large differences in the lengths of two carbon-oxygen bonds sharing a common carbon atom. 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":26962,"position":4},"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":24019,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24019","url_meta":{"origin":26962,"position":5},"title":"More record breakers for the anomeric effect involving C-N bonds.","author":"Henry Rzepa","date":"September 4, 2021","format":false,"excerpt":"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.\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\/N-C-O-distances-1024x758.jpg?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\/26962","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=26962"}],"version-history":[{"count":18,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26962\/revisions"}],"predecessor-version":[{"id":26996,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26962\/revisions\/26996"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26962"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26962"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26962"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=26962"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}