{"id":28773,"date":"2025-06-01T08:20:34","date_gmt":"2025-06-01T07:20:34","guid":{"rendered":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28773"},"modified":"2025-06-01T10:03:36","modified_gmt":"2025-06-01T09:03:36","slug":"cyclo-s6-hexathiane-anomeric-effects-again","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28773","title":{"rendered":"Cyclo-S6 (Hexathiane) &#8211; anomeric effects again!"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"28773\">\n<p>I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems\u00a0that I had described had an odd number of atoms and that I had not looked at any even numbered rings. Thus <a href=\"https:\/\/en.wikipedia.org\/wiki\/Hexasulfur\" target=\"_blank\" rel=\"noopener\">hexasulfur<\/a> is a smaller (known) ring version of S<sub>8<\/sub>, the latter by far the best known allotrope of this element of course.<\/p>\n<p>Its crystal structure<span id=\"cite_ITEM-28773-0\" name=\"citation\"><a href=\"#ITEM-28773-0\">[1]<\/a><\/span> shows it has D<sub>3d<\/sub> symmetry, with six identical S-S bond lengths of 2.068\u00c5. A MN15-L\/Def2-TZVPP calculation<span id=\"cite_ITEM-28773-1\" name=\"citation\"><a href=\"#ITEM-28773-1\">[2]<\/a><\/span> replicates this pretty well.<br \/>\n<img decoding=\"async\" class=\"aligncenter size-full wp-image-28776\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/06\/S6-D3d.jpg\" alt=\"\" width=\"400\" \/><br \/>\nSince anomeric effects manifest in crystal structures by unequal bond lengths, at first sight it seemed unlikely that this ring could be shown to exhibit them. But wait, another conformation can be found, what in cyclohexane would be called the twist-boat. It is however around 12 kcal\/mol higher in free energy than the stable form.<span id=\"cite_ITEM-28773-2\" name=\"citation\"><a href=\"#ITEM-28773-2\">[3]<\/a><\/span> and has lower (chiral) D<sub>2<\/sub> symmetry. This now shows two slightly shorter bonds and four slightly longer bonds. The anomeric NBO E(2) perturbation energies are a relatively modest 7.93 kcal\/mol (S1<sub>Lp<\/sub>-S2-S6<sub>\u03c3*<\/sub>) resulting in modest S1-S2 bond shortening and comensurate S2-S6 lengthening. By symmetry, three other identical effects manifest.<br \/>\n<img decoding=\"async\" onclick=\"jmolApplet([450,450],'load wp-content\/uploads\/2025\/06\/S6-D2.log;frame 18;set antialiasDisplay ON;measure 1 2;measure 2 6;measure 6 5;measure 5 3;measure 3 4;measure 4 1;vectors on;vectors 4;vectors scale 8.0;color vectors green;vibration 6;','c20');\" class=\"aligncenter size-full wp-image-28775\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/06\/S6-D2.jpg\" alt=\"\" width=\"400\" \/><br \/>\nSo these stereoelectronic effects CAN manifest in even-numbered rings, but only in this case as a higher energy conformer.<\/p>\n<p>I also show O<sub>6<\/sub>, with C<sub>2<\/sub> symmetry. As with O<sub>7<\/sub> and O<sub>5<\/sub> discussed previously<span id=\"cite_ITEM-28773-3\" name=\"citation\"><a href=\"#ITEM-28773-3\">[4]<\/a><\/span> the anomeric effect promotes (partial) dissociation into three molecules of O<sub>2<\/sub><span id=\"cite_ITEM-28773-4\" name=\"citation\"><a href=\"#ITEM-28773-4\">[5]<\/a><\/span>, but this process is not complete (computationally) \u00a0and weak partial bonds of ~1.997 and 2.06\u00c5 remain between the three O<sub>2<\/sub> species, which are probably in fact artefacts of using a single-determinantal wavefunction.\u00a0However it is fun to observe that the NBO E(2) terms are now (O1<sub>Lp<\/sub>-O5-O6<sub>\u03c3*<\/sub>)<strong>\u00a0135<\/strong> kcal\/mol and the even larger (O2<sub>Lp<\/sub>-O3-O4<sub>\u03c3*<\/sub>) <strong>218<\/strong> kcal\/mol (tending to \u221e for a fully broken bond). These absurdly large values are a consequence of the non-converging perturbation expansion, but they are still amusing to see.<br \/>\n<img decoding=\"async\" onclick=\"jmolApplet([450,450],'load wp-content\/uploads\/2025\/06\/O6-C2.log;frame 20;set antialiasDisplay ON;measure 1 2;measure 2 3;measure 6 3;measure 5 6;measure 5 4;measure 4 1;vectors on;vectors 4;vectors scale 8.0;color vectors green;vibration 6;','c20');\"  class=\"aligncenter size-full wp-image-28778\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/06\/O2-C2.jpg\" alt=\"\" width=\"540\" \/><br \/>\nIf you want to see the orbital interactions (as shown on the earlier blogs on this topic), why not download the wavefunction (<a href=\"https:\/\/data.hpc.imperial.ac.uk\/resolve\/?doi=15260&#038;file=3\" target=\"_blank\">the .fchk file<\/a>) from the repository archive at the\u00a0DOIs shown above and reveal them for yourself using suitable programs (the free <a href=\"https:\/\/two.avogadro.cc\">Avogadro2 program<\/a> is one that can do this exceedingly well). After this, I hesitate to say I will not find some other aspects of small sulfur and oxygen rings to write about, but other topics call for the time being!<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-28773-0\">J. Steidel, J. Pickardt, and R. Steudel, \"Redetermination of the Crystal and Molecular Structure of Cyclohexasulfur, S&lt;sub&gt;6&lt;\/sub&gt; [1]\", <i>Zeitschrift f\u00fcr Naturforschung B<\/i>, vol. 33, pp. 1554-1555, 1978. <a href=\"https:\/\/doi.org\/10.1515\/znb-1978-1238\">https:\/\/doi.org\/10.1515\/znb-1978-1238<\/a>\n\n<\/li>\n<li id=\"ITEM-28773-1\">H. Rzepa, \"S6, D3d, NBO7 G =-2388.986031\", 2025. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/15261\">https:\/\/doi.org\/10.14469\/hpc\/15261<\/a>\n\n<\/li>\n<li id=\"ITEM-28773-2\">H. Rzepa, \"S6, D2, NBO7 G = -2388.966504 DG = +12.25\", 2025. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/15260\">https:\/\/doi.org\/10.14469\/hpc\/15260<\/a>\n\n<\/li>\n<li id=\"ITEM-28773-3\">H. Rzepa, \"Cyclo-Heptasulfur, S&lt;sub&gt;7&lt;\/sub&gt; \u2013 a classic anomeric effect discovered during a pub lunch!\", 2025. <a href=\"https:\/\/doi.org\/10.59350\/rzepa.28407\">https:\/\/doi.org\/10.59350\/rzepa.28407<\/a>\n\n<\/li>\n<li id=\"ITEM-28773-4\">H. Rzepa, \"O6 NBO C2, G = -450.664220\", 2025. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/15259\">https:\/\/doi.org\/10.14469\/hpc\/15259<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 28773 -->","protected":false},"excerpt":{"rendered":"<p>I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems\u00a0that I had described had an odd number of atoms and that I had not looked at any even numbered rings. Thus hexasulfur is a smaller (known) ring version of S8, the latter by far [&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,"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":[4],"tags":[],"ppma_author":[2661],"class_list":["post-28773","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Cyclo-S6 (Hexathiane) - anomeric effects again! - Henry Rzepa&#039;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=28773\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Cyclo-S6 (Hexathiane) - anomeric effects again! - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"I thought I was done with exploring anomeric effects in small sulfur rings. However, I then realised that all the systems\u00a0that I had described had an odd number of atoms and that I had not looked at any even numbered rings. 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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 &quot;crystal_structure_mining&quot;","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":28615,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28615","url_meta":{"origin":28773,"position":1},"title":"5-Imino-5\u03bb4-heptathiepane 3-oxide. More exuberent anomeric effects.","author":"Henry Rzepa","date":"May 20, 2025","format":false,"excerpt":"The two previous \u00a0posts, on the topic of anomeric effects in 7-membered sulfur rings illustrated how orbital interactions between the lone pairs in the molecules and S-S bonds produced widely varying S-S bond lengths in the molecules, some are shorter than normal (which is ~2.05\u00c5 for e.g. the S8 ring)\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":26962,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26962","url_meta":{"origin":28773,"position":2},"title":"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents.","author":"Henry Rzepa","date":"April 30, 2024","format":false,"excerpt":"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\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":12276,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12276","url_meta":{"origin":28773,"position":3},"title":"Artemisinin: are stereo-electronics at the core of its (re)activity?","author":"Henry Rzepa","date":"April 13, 2014","format":false,"excerpt":"Around 100 tons of the potent antimalarial artemisinin is produced annually; a remarkable quantity given its very unusual and fragile looking molecular structure (below). When I looked at this, I was immediately struck by a thought: surely this is a classic molecule for analyzing stereoelectronic effects (anomeric and gauche). Here\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"artemisinin1","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/04\/artemisinin1.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":28773,"position":4},"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 &quot;crystal_structure_mining&quot;","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":28515,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28515","url_meta":{"origin":28773,"position":5},"title":"Cycloheptasulfur sulfoxide, S7O &#8211; Anomeric effects galore!","author":"Henry Rzepa","date":"May 19, 2025","format":false,"excerpt":"The monosulfoxide of cyclo-heptasulfur was reported along with cycloheptasulfur itself in 1977, along with the remarks that \"The \u03b4 modification of S7 contains bonds of widely differing length: this has never been observed before in an unsubstituted molecule. and \"the same effect having also been observed in other sulfur rings\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":[]}],"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\/28773","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=28773"}],"version-history":[{"count":21,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/28773\/revisions"}],"predecessor-version":[{"id":28800,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/28773\/revisions\/28800"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=28773"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=28773"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=28773"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=28773"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}