{"id":16671,"date":"2016-08-06T15:34:07","date_gmt":"2016-08-06T14:34:07","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16671"},"modified":"2016-09-17T07:52:19","modified_gmt":"2016-09-17T06:52:19","slug":"a-periodic-table-for-anomeric-centres","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16671","title":{"rendered":"A periodic table for anomeric centres."},"content":{"rendered":"
\n

In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures.<\/p>\n

The effect is defined by X bearing two substituents, one of which Z is a centre bearing a “lone pair” of electrons (or two electrons in a \u03c0-bond<\/a>), and another Y in which the X-Y bond has a low-lying acceptor or \u03c3* empty orbital into which the lone pair can be donated. This donation will only occur if the Z-lone pair and the X-Y bond vectors align antiperiplanar. Here is the summary so far.<\/p>\n\n\n\n\n\n\n\n\n\n\n
X<\/th>\nBlog entry<\/th>\n<\/tr>\n
B<\/td>\n16601<\/a><\/td>\n<\/tr>\n
C<\/td>\n14508<\/a>,8898<\/a><\/td>\n<\/tr>\n
N<\/td>\nthis one<\/td>\n<\/tr>\n
O<\/td>\n16646<\/a><\/td>\n<\/tr>\n
Si<\/td>\n16601<\/a><\/td>\n<\/tr>\n
P<\/td>\n16601<\/a><\/td>\n<\/tr>\n
S<\/td>\nthis one<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

As required of a good periodic table, it has gaps that need completing, in this case X=N and X=S. Firstly N, for which the small molecule below is known (FUHFAP).<\/p>\n

\"FUHFAP\" <\/p>\n

A \u03c9B97XD\/Def2-TZVPP calculation[1]<\/a><\/span> yields an electron density distribution, which can be collected into monosynaptic basins using the ELF technique. There are two oxygen lone pairs (17 and 20) that are close to antiperiplanar to the adjacent N-O bond, having E(2) interaction energies obtained using the NBO method of 15.1 and 15.8 kcal\/mol, typical of the anomeric range. The basin labelled 13 on X=N1 below is also perfectly aligned antiperiplanar with the adjacent O3-C2 bond, but its E(2) interaction energy is only 7.3 kcal\/mol. Thus a strong anomeric interaction on the anomeric atom itself does not seem to occur. The same effect was noted for X=O in the previous post; the explanation remains unidentified.<\/p>\n

\"FUHFAP\"<\/p>\n

With the X=S gap, we have lots of opportunity with polysulfide compounds, a good example of which is the C2<\/sub>-symmetric and helical S8<\/sub> dianion TEGWAF[2]<\/a><\/span><\/p>\n

\"TEGWAF\"<\/p>\n

Each of the 8 sulfur atoms exhibits antiperiplanar orientation of an S lone pair with an adjacent S-S acceptor σ* orbital;
\n1:2-3=23.7 kcal\/mol;
\n2:3-4=18.5;
\n3:4-8=11.7, 3:2-1=7.4;
\n4:8-7=11.4, 4:3-2=9.2.<\/p>\n

This just surveys the central main group elements, and it is possible that this little mini-periodic table may yet grow.<\/p>\n

References<\/h2>\n
  1. H.S. Rzepa, \"C 2 H 7 N 1 O 2\", 2016. https:\/\/doi.org\/10.14469\/ch\/195294<\/a>\n\n<\/li>\n
  2. Rybak, W.K.., Cymbaluk, A.., Skonieczny, J.., and Siczek, M.., \"CCDC 880780: Experimental Crystal Structure Determination\", 2012. https:\/\/doi.org\/10.5517\/ccykj88<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. 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 centre bearing a “lone pair” […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":true,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_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},"jetpack_post_was_ever_published":false},"categories":[1745,4],"tags":[1842,1562,1469,260,1676,1465,1466,1402,1395,41,1518,1442,1560],"ppma_author":[2661],"class_list":["post-16671","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry","tag-acetals","tag-alkane-stereochemistry","tag-anomer","tag-anomeric-effect","tag-atomic-orbital","tag-carbohydrate-chemistry","tag-carbohydrates","tag-chemical-bond","tag-chemistry","tag-interaction-energy","tag-lone-pair","tag-physical-organic-chemistry","tag-stereochemistry"],"yoast_head":"\nA periodic table for anomeric centres. - 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=16671\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A periodic table for anomeric centres. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. 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 centre bearing a “lone pair” […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16671\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-08-06T14:34:07+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-09-17T06:52:19+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/08\/FUHFAP.svg\" \/>\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 periodic table for anomeric centres. - 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=16671","og_locale":"en_GB","og_type":"article","og_title":"A periodic table for anomeric centres. - Henry Rzepa's Blog","og_description":"In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures. 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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\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":"","width":0,"height":0},"classes":[]},{"id":16696,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","url_meta":{"origin":16671,"position":1},"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":16601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16601","url_meta":{"origin":16671,"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":745,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=745","url_meta":{"origin":16671,"position":3},"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":16610,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610","url_meta":{"origin":16671,"position":4},"title":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens.","author":"Henry Rzepa","date":"July 8, 2016","format":false,"excerpt":"The previous post looked at anomeric effects set up on centres such as B, Si or P, and involving two oxygen groups attached to these atoms. Here I vary the attached groups to include either one or two nitrogen atoms..The\u00a0plot below shows aminols, C(NHR)(OR\"). A torsion along either the C-O\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":"aminol","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/07\/aminol-1-1024x773.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":22471,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22471","url_meta":{"origin":16671,"position":5},"title":"Fascinating stereoelectronic control in Metaldehyde and Chloral.","author":"Henry Rzepa","date":"June 9, 2020","format":false,"excerpt":"Metaldehyde is an insecticide used to control slugs. When we unsuccessfully tried to get some recently, I discovered it is now deprecated in the UK. So my immediate reaction was to look up its structure to see if that cast any light (below, R=CH3, shown as one stereoisomer). A X-ray\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":[]}],"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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16671","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=16671"}],"version-history":[{"count":21,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16671\/revisions"}],"predecessor-version":[{"id":16703,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16671\/revisions\/16703"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16671"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16671"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16671"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16671"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}