{"id":26896,"date":"2024-03-18T16:52:41","date_gmt":"2024-03-18T16:52:41","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=26896"},"modified":"2024-03-18T17:02:01","modified_gmt":"2024-03-18T17:02:01","slug":"detecting-anomeric-effects-in-tetrahedral-carbon-bearing-four-oxygen-substituents","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26896","title":{"rendered":"Detecting anomeric effects in tetrahedral carbon bearing four oxygen substituents."},"content":{"rendered":"
\n

I have written a few times about the so-called “anomeric effect<\/a>“, 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 when one of these bonds has a very different length from the other. The effect originates when one of the lone pair of electrons on one oxygen atom uniquely overlaps with the C-O antibonding \u03c3*<\/sup> on another oxygen, thus shortening the length of the donating oxygen-carbon length and lengthening the length of accepting C-O bond. Here I take a look at tetra-substituted versions of this (C(OR)4<\/sub>), where in theory there are up to eight lone pairs, interacting with any of three C-O bonds, giving a total of 24 possible anomeric effects in one molecule.<\/p>\n

\"\"<\/a>
\nWe start the process with a search of the Cambridge crystal structure database, using the following search query:
\n\"\"<\/p>\n

This yields 25 hits. We now want to find out what the longest and shortest C-O bonds are, and how large the difference between them is. To do this, we have to resort to applying some functions, using the calculator tool built into the Mercury analysis software. The following functions were used:<\/p>\n

    \n
  1. Greatest('search3'.'DIST1','search3'.'DIST2','search3'.'DIST3','search3'.'DIST4')<\/tt><\/small><\/li>\n
  2. Least('search3'.'DIST1','search3'.'DIST2','search3'.'DIST3','search3'.'DIST4')<\/tt><\/small><\/li>\n
  3. Greatest('search3'.'DIST1', 'search3'.'DIST2', 'search3'.'DIST3', 'search3'.'DIST4')-Least('search3'.'DIST1', 'search3'.'DIST2', 'search3'.'DIST3', 'search3'.'DIST4')<\/tt><\/small>
    \n\"\"
    \n\"\"<\/li>\n<\/ol>\n

    The results can be displayed as below, in which the difference between the two bond lengths is colour coded (red = greatest, blue = least).
    \n\"\"<\/p>\n

      \n
    1. Here you can see that when the difference between the longest and short C-O bond lengths is small, the colour is blue.<\/li>\n
    2. Green dots show a difference of about 0.04-0.05\u00c5<\/li>\n
    3. The red dot has the greatest difference of 0.087\u00c5 and corresponds to the entry SILDOH ([1]<\/a><\/span>, DataDOI: [2]<\/a><\/span>, 10.5517\/ccq8lq8<\/a>.<\/li>\n<\/ol>\n

      The next step is to apply a “reality check” using computation, here a MN15L\/Def2-TZVPP calculation on the top eight entries as sorted by the largest C-O bond length differences (\u0394rC-O<\/sub> > 0.05\u00c5.[3]<\/a><\/span>, data DOI: 10.14469\/hpc\/13925<\/a><\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n
      CCDC Ref code<\/th>\nCrystal structure<\/th>\nComputational structure<\/th>\n<\/tr>\n
      Longest<\/th>\nShortest<\/th>\n\u0394<\/th>\nLongest<\/th>\nshortest<\/th>\n\u0394<\/th>\n<\/tr>\n
      SILDOH<\/td>\n1.451<\/td>\n1.364<\/td>\n0.087<\/td>\n1.441<\/td>\n1.367<\/td>\n0.074<\/td>\n<\/tr>\n
      PILTOU<\/td>\n1.432<\/td>\n1.361<\/td>\n0.071<\/td>\n1.418<\/td>\n1.378<\/td>\n0.040<\/td>\n<\/tr>\n
      GISSAD<\/td>\n1.435<\/td>\n1.367<\/td>\n0.068<\/td>\n1.422<\/td>\n1.375<\/td>\n0.047<\/td>\n<\/tr>\n
      BODGEG<\/td>\n1.507<\/td>\n1.442<\/td>\n0.065<\/td>\n1.424<\/td>\n1.370<\/td>\n0.054<\/td>\n<\/tr>\n
      GINLOF<\/td>\n1.425<\/td>\n1.364<\/td>\n0.061<\/td>\n1.418<\/td>\n1.377<\/td>\n0.041<\/td>\n<\/tr>\n
      POCPOO<\/td>\n1.419<\/td>\n1.361<\/td>\n0.058<\/td>\n1.421<\/td>\n1.371<\/td>\n0.050<\/td>\n<\/tr>\n
      KEVFUM<\/td>\n1.417<\/td>\n1.361<\/td>\n0.056<\/td>\n1.395<\/td>\n1.391<\/td>\n0.004<\/td>\n<\/tr>\n
      AHEYAO<\/td>\n1.423<\/td>\n1.370<\/td>\n0.053<\/td>\n1.422<\/td>\n1.372<\/td>\n0.050<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
        \n
      1. The largest effect occurs for SILDOH, and this is replicated by calculation.<\/li>\n
      2. The largest discrepancy between measurement and calculation is for KEVFUM, \u00a0where calculation predicts almost no C-O bond differences. This will be discussed elsewhere.<\/li>\n<\/ol>\n

        Focusing on SILDOH,\u00a0we look at the\u00a0NBO E(2) energies for the donor-acceptor interactions of an oxygen lone pair donating into a C-O antibonding \u03c3*<\/sup> orbital.<\/p>\n

        \"\"<\/p>\n

        Click on the image below for a 3D model of the two interacting orbitals (positive overlap = blue + purple, red + orange) <\/p>\n

        \"\"<\/p>\n

        \nThe interaction of LpO1 to the long bond C5-O4 = 18.0<\/strong> and LpO2 to C5-O4 = 16.3<\/strong> kcal\/mol, whereas in the reverse directions, LpO4 to C5-O1 is only 6.0<\/strong> kcal\/mol and LpO4 to C5-O2 is 10.7<\/strong> kcal\/mol. \u00a0For a “normal” C-O bond however such as \u00a0C5-O3, \u00a0LpO2 to C5-O3 = 3.1<\/strong> and LPO1 to C5-O3 = 5.3<\/strong> kcal\/mol. In effect, two oxygens “gang up” on weakening the \u00a0long C5-O4 bond,\u00a0but leave the shorter C5-O3 bond alone. So the individual anomeric effects are no larger than normal, but the cooperative effect of two acting together is what produces the final geometric asymmetry.\n<\/p>\n

        \nThe Wiberg bond index mirrors this effect. The bond indices are 0.9882<\/strong> for O1-C5 and C5-O4 0.8512<\/strong> (\u0394 =-0.137<\/strong>) which is a big difference in bond order and accounting for the large (record?) difference in bond length.\n<\/p>\n

        \nIn the next post, I will analyse the equivalent molecules B(OR)4<\/sub>–<\/sup>.<\/p>\n

        References<\/h2>\n
        1. R. Betz, and P. Kl\u00fcfers, \"Norbornane-2,7-diyl 1\u2032,2\u2032-phenylene orthocarbonate\", Acta Crystallographica Section E Structure Reports Online<\/i>, vol. 63, pp. o3933-o3933, 2007. https:\/\/doi.org\/10.1107\/s1600536807042298<\/a>\n\n<\/li>\n
        2. Betz, R.., and Klufers, P.., \"CCDC 663670: Experimental Crystal Structure Determination\", 2007. https:\/\/doi.org\/10.5517\/ccq8lq8<\/a>\n\n<\/li>\n
        3. H. Rzepa, \"Detecting anomeric effects in tetrahedral carbon bearing four oxygen substituents.\", 2024. https:\/\/doi.org\/10.14469\/hpc\/13925<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

          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 when one of these bonds […]<\/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":[2648],"ppma_author":[2661],"class_list":["post-26896","post","type-post","status-publish","format-standard","hentry","tag-interesting-chemistry"],"yoast_head":"\nDetecting anomeric effects in tetrahedral carbon 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=26896\" \/>\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 carbon bearing four oxygen substituents. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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. 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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\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.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\/04\/Screenshot-304.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":5368,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5368","url_meta":{"origin":26896,"position":1},"title":"Spotting the unexpected. Anomeric effects involving alkenes?","author":"Henry Rzepa","date":"November 2, 2011","format":false,"excerpt":"How one might go about answering the question: do alkenes promote anomeric effects? A search of chemical abstracts does not appear to cite any examples (I may have missed them of course, since it depends very much on the terminology you use, and new effects may not yet have any\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/11\/query.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16601","url_meta":{"origin":26896,"position":2},"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":[]},{"id":23973,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23973","url_meta":{"origin":26896,"position":3},"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":24019,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24019","url_meta":{"origin":26896,"position":4},"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":[]},{"id":6361,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6361","url_meta":{"origin":26896,"position":5},"title":"Spotting the unexpected. The trifluoromeric effect in the hydration of the carbonyl group.","author":"Henry Rzepa","date":"March 9, 2012","format":false,"excerpt":"The equilibrium for the hydration of a ketone to form a gem-diol hydrate is known to be highly sensitive to substituents. Consider the two equilibria: For propanone, it lies almost entirely on the left, whereas for the hexafluoro derivative it is almost entirely on the right. The standard answer 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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/03\/diol.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\/26896","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=26896"}],"version-history":[{"count":30,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26896\/revisions"}],"predecessor-version":[{"id":26940,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26896\/revisions\/26940"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26896"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26896"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26896"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=26896"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}