{"id":16696,"date":"2016-08-08T10:12:17","date_gmt":"2016-08-08T09:12:17","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16696"},"modified":"2016-09-17T07:51:54","modified_gmt":"2016-09-17T06:51:54","slug":"a-periodic-table-for-anomeric-centres-this-time-with-quantified-interactions","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","title":{"rendered":"A periodic table for anomeric centres, this time with quantified interactions."},"content":{"rendered":"
\n

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<\/strong>, where X<\/strong> is of two types:<\/p>\n

    \n
  1. A two-coordinate atom across the series B-O and Al-S, and carrying the appropriate molecular charge such that X carries two lone pairs of electrons (thus the charge is 0 for O, but -3 for B).<\/li>\n
  2. A four-coordinate atom across the series B-O and Al-S, with X-H bonds replacing the lone pairs on this centre in the previous example, and again with appropriate molecule charges (e.g.<\/em> +2 for \u00a0SH2<\/sub>).<\/li>\n<\/ol>\n

    The donor in the anomeric interaction always originates on the oxygen of the MeO group attached to X. The acceptor is always the X-O\u00a0\u03c3* empty orbital. The results (table below, \u03c9B97XD\/Def2-TZVPP calculation, NBO E(2) in kcal\/mol) confirm that as X gets more electronegative, the X-O\u00a0\u03c3* empty orbital becomes a better acceptor, and so the NBO E(2) interaction energy which quantifies the anomeric interaction gets larger. Eventually (with X=OH2<\/sub>) the donation of electrons into the X-O\u00a0\u03c3* empty orbital becomes so effective that the X-O bond (in this case O-O) dissociates fully and the NBO perturbation cannot be computed. Also for reference, a “normal” anomeric interaction (such as is found in e.g.<\/em> sugars) is around 18 kcal\/mol. Anything larger than this could be considered especially strong, and anything less than ~10 kcal\/mol would be regarded as weak.\u00a0<\/p>\n\n\n\n\n\n\n\n\n\n\n\n
    X[1]<\/a><\/span>*<\/th>\n<\/tr>\n
    BH2<\/sub><\/td>\nCH2<\/sub><\/td>\nNH2<\/sub><\/td>\nOH2<\/sub><\/td>\n<\/tr>\n
    12.5<\/td>\n17.7<\/td>\n18.5<\/td>\ndissociates<\/td>\n<\/tr>\n
    AlH2<\/sub><\/td>\nSiH2<\/sub><\/td>\nPH2<\/sub><\/td>\nSH2<\/sub><\/td>\n<\/tr>\n
    6.9<\/td>\n12.9<\/td>\n21.9<\/td>\n31.3<\/td>\n<\/tr>\n
    B<\/td>\nC<\/td>\nN<\/td>\nO<\/td>\n<\/tr>\n
    8.3<\/td>\n11.7<\/td>\n12.9<\/td>\n14.2<\/td>\n<\/tr>\n
    Al<\/td>\nSi<\/td>\nP<\/td>\nS<\/td>\n<\/tr>\n
    4.8<\/td>\n6.6<\/td>\n11.2<\/td>\n18.2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    For the\u00a0entry X=S, the E(2) term is actually larger than for the oxygen. I should note that the Me group itself is not passive in this process. The C-H bonds can also act as significant electron donors, but here I am not going to analyse this additional complexity.<\/p>\n

    This table reveals that there is nothing special about carbon as an anomeric centre, and here also\u00a0the normal intimate association with the term anomeric and\u00a0heterocyclohexanes such as found in sugars.<\/p>\n

    \n

    * Here I introduce a refinement to my normal process of citing the data produced for any specific calculation. Rather than including 16 individual citations for each cell in the table, I have gathered all these calculations into a collection and cite here only the DOI of that collection. When resolved, the individual members of that collection can then be inspected for the actual data.<\/p>\n

    References<\/h2>\n
    1. H. Rzepa, \"Anomeric interactions at atom centres\", 2016. https:\/\/doi.org\/10.14469\/hpc\/1221<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      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 Al-S, and carrying the […]<\/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":true,"_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":[1469,260,1676,1465,1466,1402,557,1395,1449,41,1518,1442,1512],"ppma_author":[2661],"class_list":["post-16696","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-anomer","tag-anomeric-effect","tag-atomic-orbital","tag-carbohydrate-chemistry","tag-carbohydrates","tag-chemical-bond","tag-chemical-bonding","tag-chemistry","tag-hydrogen-bond","tag-interaction-energy","tag-lone-pair","tag-physical-organic-chemistry","tag-quantum-chemistry"],"yoast_head":"\nA periodic table for anomeric centres, this time with quantified interactions. - 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=16696\" \/>\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, this time with quantified interactions. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 Al-S, and carrying the […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-08-08T09:12:17+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-09-17T06:51:54+00:00\" \/>\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, this time with quantified interactions. - 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=16696","og_locale":"en_GB","og_type":"article","og_title":"A periodic table for anomeric centres, this time with quantified interactions. - Henry Rzepa's Blog","og_description":"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 Al-S, and carrying the […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","og_site_name":"Henry Rzepa's Blog","article_published_time":"2016-08-08T09:12:17+00:00","article_modified_time":"2016-09-17T06:51:54+00:00","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=16696#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"A periodic table for anomeric centres, this time with quantified interactions.","datePublished":"2016-08-08T09:12:17+00:00","dateModified":"2016-09-17T06:51:54+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696"},"wordCount":429,"commentCount":0,"keywords":["Anomer","Anomeric effect","Atomic orbital","Carbohydrate chemistry","Carbohydrates","Chemical bond","chemical bonding","Chemistry","Hydrogen bond","interaction energy","Lone pair","Physical organic chemistry","Quantum chemistry"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","name":"A periodic table for anomeric centres, this time with quantified interactions. - Henry Rzepa's Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"datePublished":"2016-08-08T09:12:17+00:00","dateModified":"2016-09-17T06:51:54+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"A periodic table for anomeric centres, this time with quantified interactions."}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa's Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-4li","jetpack-related-posts":[{"id":16671,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16671","url_meta":{"origin":16696,"position":0},"title":"A periodic table for anomeric centres.","author":"Henry Rzepa","date":"August 6, 2016","format":false,"excerpt":"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\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":16696,"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":14508,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508","url_meta":{"origin":16696,"position":2},"title":"A visualization of the anomeric effect from crystal structures.","author":"Henry Rzepa","date":"August 27, 2015","format":false,"excerpt":"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\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":2207,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207","url_meta":{"origin":16696,"position":3},"title":"Tunable bonds looked at in a different way","author":"Henry Rzepa","date":"July 11, 2010","format":false,"excerpt":"The title of this post merges those of the two previous ones. The tunable C-Cl bond brought about in the molecule tris(amino)chloromethane by anomeric effects will be probed using the Laplacian of the electronic density. The figure above shows the Laplacian for a conformation of tris(amino)chloromethane with one of the\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.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/app-1-0.67.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":16696,"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":745,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=745","url_meta":{"origin":16696,"position":5},"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":[]}],"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\/16696","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=16696"}],"version-history":[{"count":6,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16696\/revisions"}],"predecessor-version":[{"id":16702,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16696\/revisions\/16702"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16696"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16696"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16696"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16696"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}