{"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":"2015-08-27T15:17:19","modified_gmt":"2015-08-27T14:17:19","slug":"a-visualization-of-the-anomeric-effect-from-crystal-structures","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/blog\/?p=14508","title":{"rendered":"A visualization of the anomeric effect from crystal structures."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"14508\">\n<p>The <a href=\"https:\/\/en.wikipedia.org\/wiki\/Anomer\" target=\"_blank\">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\u00b0, one oxygen lone pair can donate into the C-O \u03c3* empty orbital and a stabilisation occurs. Here I explore whether crystal structures reflect this effect.<\/p>\n<p><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/anomeric.jpg?w=440\" alt=\"Scheme\"  \/><\/p>\n<p>The 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 &lt; 5%, no disorder and no errors specified.<\/p>\n<ol>\n<li>You can see from the plot below that the hotspot occurs when <strong>both<\/strong> RO-CO torsions are ~65\u00b0. From this we will assume that the two (unseen)<sup>\u2021<\/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\u00b0 with respect to the same RO-CO bond (the other is therefore oriented -60\u00b0). This allows it to be antiperiplanar to the adjacent C-O bond and hence interact with its \u03c3* empty orbital. So the hotspot corresponds to structures where BOTH oxygen atoms have lone pairs which interact with the adjacent O-C anti bond.<\/li>\n<li>There is a tiny cluster for which\u00a0<strong>both<\/strong>\u00a0RO-CO torsions are ~180\u00b0 and hence neither oxygen has an antiperiplanar lone pair.<\/li>\n<li>Only slightly larger are clusters where one torsion is\u00a0~65\u00b0 and the other\u00a0~180\u00b0, meaning that only one oxygen has an antiperiplanar lone pair.<\/li>\n<li>A plot of the two C-O lengths indeed shows an overall hotspot at ~1.40\u00c5 for both distances. If the search is filtered to include only torsions in the range 150-180\u00b0, the hotspot value increases to 1.415\u00c5 for both. If one torsion is restricted to 40-80\u00b0 and the other to\u00a0150-180\u00b0 the hotspot shows one C-O bond is about 0.012\u00c5 shorter than the other.<\/li>\n<\/ol>\n<p><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/rocor-tor.jpg?w=440\" alt=\"Scheme\"  \/><\/p>\n<p><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/rocor-dist.jpg?w=440\" alt=\"Scheme\"  \/><\/p>\n<p>I also include a further constraint, that the diffraction data must be collected below 140K. The hotspot moves to ~ 55\/60\u00b0 indicating values free of some vibrational noise.<\/p>\n<p><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/rocor-140.jpg?w=440\" alt=\"Scheme\"  \/><\/p>\n<p>Interestingly, replacing \u00a0oxygen with \u00a0nitrogen reveals relatively few examples of the effect (C(NR<sub>2<\/sub>)<sub>4<\/sub> is an exception). Replacing \u00a0O 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.<\/p>\n<p><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/rscsr-tor.jpg?w=440\" alt=\"Scheme\"  \/><\/p>\n<hr \/>\n<p><sup>\u2021<\/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.<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 14508 -->","protected":false},"excerpt":{"rendered":"<p>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\u00b0, one oxygen lone pair can donate into the C-O \u03c3* empty orbital and a stabilisation occurs. Here I [&hellip;]<\/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,"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":[3,1754],"tags":[1556,33,1410,1411,1563,1414,1447,1478,1497,1500,1610,1510],"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"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p1gPyz-3M0","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14508","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=14508"}],"version-history":[{"count":0,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14508\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14508"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14508"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14508"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}