{"id":14508,"date":"2015-08-27T15:17:19","date_gmt":"2015-08-27T14:17:19","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14508"},"modified":"2023-09-17T07:17:48","modified_gmt":"2023-09-17T06:17:48","slug":"a-visualization-of-the-anomeric-effect-from-crystal-structures","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508","title":{"rendered":"A visualization of the anomeric effect from crystal structures."},"content":{"rendered":"
\n

\n\tThe anomeric effect<\/a> is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I explore whether crystal structures reflect this effect.\n<\/p>\n

\n\t\"Scheme\"\n<\/p>\n

\n\tThe torsion angles along each O-C bond are specified, along with the two C-O distances. All the bonds are declared acyclic, and the usual R < 5%, no disorder and no errors specified.\n<\/p>\n

    \n
  1. \n\t\tYou can see from the plot below that the hotspot occurs when both<\/strong> RO-CO torsions are ~65°. From this we will assume that the two (unseen)‡<\/sup> lone pairs at any one of the oxygens are distributed approximately tetrahedrally around each oxygen, and if this is true then one of them must by definition be oriented ~ 180° with respect to the same RO-CO bond (the other is therefore oriented -60°). This allows it to be antiperiplanar to the adjacent C-O bond and hence interact with its σ* empty orbital. So the hotspot corresponds to structures where BOTH oxygen atoms have lone pairs which interact with the adjacent O-C anti bond.\n\t<\/li>\n
  2. \n\t\tThere is a tiny cluster for which both<\/strong> RO-CO torsions are ~180° and hence neither oxygen has an antiperiplanar lone pair.\n\t<\/li>\n
  3. \n\t\tOnly slightly larger are clusters where one torsion is ~65° and the other ~180°, meaning that only one oxygen has an antiperiplanar lone pair.\n\t<\/li>\n
  4. \n\t\tA plot of the two C-O lengths indeed shows an overall hotspot at ~1.40Å for both distances. If the search is filtered to include only torsions in the range 150-180°, the hotspot value increases to 1.415Å for both. If one torsion is restricted to 40-80° and the other to 150-180° the hotspot shows one C-O bond is about 0.012Å shorter than the other.\n\t<\/li>\n<\/ol>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n\tI also include a further constraint, that the diffraction data must be collected below 140K. The hotspot moves to ~ 55\/60° indicating values free of some vibrational noise.\n<\/p>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n\tInterestingly, replacing  oxygen with  nitrogen reveals relatively few examples of the effect (C(NR2<\/sub>)4<\/sub> is an exception). Replacing  O by divalent S produces only 13 hits, with the surprising result (below) that in all of them only one S sets up an anomeric interaction. Arguably, the number of examples is too low to draw any firm conclusions from this observation.\n<\/p>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n

    \n\t‡<\/sup>Most diffractometers measure low angle scattering of X-rays by high density electrons. These are the core electrons associated with a nucleus rather than the valence electrons associated with lone pairs. Hence very few positions of valence lone pairs have ever been crystallographically measured.\n<\/p>\n

    \n

    Acknowledgments<\/h4>\n

    This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I […]<\/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":[2,1745],"tags":[1562,260,1465,1466,1561,1402,1445,1518,1442,1512,1560,1405],"ppma_author":[2661],"class_list":["post-14508","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-alkane-stereochemistry","tag-anomeric-effect","tag-carbohydrate-chemistry","tag-carbohydrates","tag-carbon-oxygen-bond","tag-chemical-bond","tag-ether","tag-lone-pair","tag-physical-organic-chemistry","tag-quantum-chemistry","tag-stereochemistry","tag-technologyinternet"],"yoast_head":"\nA visualization of the anomeric effect from crystal structures. - 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=14508\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A visualization of the anomeric effect from crystal structures. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-08-27T14:17:19+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-17T06:17:48+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/anomeric.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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"A visualization of the anomeric effect from crystal structures. - 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=14508","og_locale":"en_GB","og_type":"article","og_title":"A visualization of the anomeric effect from crystal structures. - Henry Rzepa's Blog","og_description":"The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508","og_site_name":"Henry Rzepa's Blog","article_published_time":"2015-08-27T14:17:19+00:00","article_modified_time":"2023-09-17T06:17:48+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/anomeric.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"A visualization of the anomeric effect from crystal structures.","datePublished":"2015-08-27T14:17:19+00:00","dateModified":"2023-09-17T06:17:48+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508"},"wordCount":474,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/anomeric.jpg","keywords":["Alkane stereochemistry","Anomeric effect","Carbohydrate chemistry","Carbohydrates","Carbon\u2013oxygen bond","Chemical bond","Ether","Lone pair","Physical organic chemistry","Quantum chemistry","Stereochemistry","Technology\/Internet"],"articleSection":["Chemical IT","crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508","name":"A visualization of the anomeric effect from crystal structures. - 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Here I try to summarise the atoms for which the effect is manifest in crystal structures. The effect is defined by X bearing two substituents, one of which Z is a\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":"","width":0,"height":0},"classes":[]},{"id":16601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16601","url_meta":{"origin":14508,"position":1},"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":745,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=745","url_meta":{"origin":14508,"position":2},"title":"Spotting the unexpected: Anomeric effects","author":"Henry Rzepa","date":"September 18, 2009","format":false,"excerpt":"Chemistry can be very focussed nowadays. This especially applies to target-driven synthesis, where the objective is to make a specified molecule, in perhaps as an original manner as possible. A welcome, but not always essential aspect of such syntheses is the discovery of new chemistry. In this blog, I will\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":"A cyano-substituted cis decalin","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/anomeric-cn.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16696,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","url_meta":{"origin":14508,"position":3},"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":16646,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16646","url_meta":{"origin":14508,"position":4},"title":"Stereoelectronic effects galore: bis(trifluoromethyl)trioxide.","author":"Henry Rzepa","date":"August 4, 2016","format":false,"excerpt":"Here is a little molecule that can be said to be pretty electron rich. There are lots of lone pairs present, and not a few electron-deficient \u03c3-bonds. I thought it might be fun to look at the stereoelectronic interactions set up in this little system. Known as ZEYDOW in 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":"","src":"","width":0,"height":0},"classes":[]},{"id":23973,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23973","url_meta":{"origin":14508,"position":5},"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":[]}],"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\/14508","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=14508"}],"version-history":[{"count":8,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14508\/revisions"}],"predecessor-version":[{"id":26494,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14508\/revisions\/26494"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14508"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14508"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14508"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14508"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}