{"id":16610,"date":"2016-07-08T11:05:33","date_gmt":"2016-07-08T10:05:33","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16610"},"modified":"2016-09-17T07:53:54","modified_gmt":"2016-09-17T06:53:54","slug":"anomeric-effects-at-carbon-involving-lone-pairs-originating-from-one-or-two-nitrogens","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610","title":{"rendered":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens."},"content":{"rendered":"
\n

The previous post <\/a>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.[1]<\/a><\/span><\/p>\n

.\"aminol-sq\"<\/p>\n

The\u00a0plot below shows aminols, C(NHR)(OR”). A torsion along either the C-O or C-N bond of ~60\u00b0 implies that (at two coordinate oxygen or three coordinated nitrogen) there may be a lone pair with a torsion of 180\u00b0, which would set up an antiperiplanar alignment between that lone pair and the adjacent C-O or C-N bond (the anomeric effect). The clear hotspot is at angles of ~80\u00b0, which does raise the issue of why it deviates from 60\u00b0. Only a location of the lone pair centroid (using eg the ELF quantum mechanical technique) would cast light on that. There is a less distinct region for which the C-N torsion is 60\u00b0\u00a0and the C-O torsion 180\u00b0, and an even less distinct region for the reverse (C-O\u00a0torsion is 60\u00b0\u00a0and the C-N\u00a0torsion 180\u00b0). This tends to imply that a nitrogen lone pair is a better donor into a C-O bond than the reverse. Electronegativity suggests this should indeed be so, with the N lone pair less bound by the N nucleus and hence easier to release into a C-O\u03c3*<\/sup>\u00a0orbital which is a better acceptor than then equivalent\u00a0C-N\u03c3*<\/sup> orbital. \"aminol\" This plot is where both heteroatoms are nitrogen (geminal diamines).\u00a0There are about twice as many examples, resulting in more distinct clustering. The anomeric hotspot is now around 70\u00b0\u00a0\u00a0and there are equally populated clusters where only one torsion is ~70\u00b0. There is another cluster for which both torsions are 180\u00b0 (no stereoelectronic alignment of lone pairs) and three small clusters where the torsions are either 180\u00b0\u00a0or 0\u00b0. There is finally an intriguing cluster for which both torsions at ~120\u00b0 (again no stereoelectronics).\u00a0\"diamine\"<\/p>\n

Searches like this seem to be good at creating more questions than they answer. Clearly, the origins of the various hotspots need to be investigated, ideally using quantum mechanics to quantify the stereoelectronic interactions involved. So this sort of (ten minute) exercise is very good at raising research project investigations.<\/p>\n

References<\/h2>\n
  1. H. Rzepa, \"Anomeric effects at carbon, involving lone pairs originating from one or two nitrogens\", 2016. https:\/\/doi.org\/10.14469\/hpc\/936<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    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 or C-N bond […]<\/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":[1745],"tags":[1469,260,1465,1886,1466,1395,1885],"ppma_author":[2661],"class_list":["post-16610","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-anomer","tag-anomeric-effect","tag-carbohydrate-chemistry","tag-carbohydrate-conformation","tag-carbohydrates","tag-chemistry","tag-nitrogen"],"yoast_head":"\nAnomeric effects at carbon involving lone pairs originating from one or two nitrogens. - 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=16610\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 or C-N bond […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-07-08T10:05:33+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-09-17T06:53:54+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/07\/aminol-sq-1.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":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens. - 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=16610","og_locale":"en_GB","og_type":"article","og_title":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens. - Henry Rzepa's Blog","og_description":"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 or C-N bond […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610","og_site_name":"Henry Rzepa's Blog","article_published_time":"2016-07-08T10:05:33+00:00","article_modified_time":"2016-09-17T06:53:54+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/07\/aminol-sq-1.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=16610#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens.","datePublished":"2016-07-08T10:05:33+00:00","dateModified":"2016-09-17T06:53:54+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610"},"wordCount":369,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/07\/aminol-sq-1.jpg","keywords":["Anomer","Anomeric effect","Carbohydrate chemistry","Carbohydrate conformation","Carbohydrates","Chemistry","Nitrogen"],"articleSection":["crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610","name":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens. - 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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":16601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16601","url_meta":{"origin":16610,"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":24019,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24019","url_meta":{"origin":16610,"position":2},"title":"More record breakers for the anomeric effect involving C-N bonds.","author":"Henry Rzepa","date":"September 4, 2021","format":false,"excerpt":"An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom. 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 "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\/N-C-O-distances-1024x758.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":23973,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23973","url_meta":{"origin":16610,"position":3},"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":[]},{"id":16671,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16671","url_meta":{"origin":16610,"position":4},"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":5368,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5368","url_meta":{"origin":16610,"position":5},"title":"Spotting the unexpected. Anomeric effects involving alkenes?","author":"Henry Rzepa","date":"November 2, 2011","format":false,"excerpt":"How one might go about answering the question: do alkenes promote anomeric effects? A search of chemical abstracts does not appear to cite any examples (I may have missed them of course, since it depends very much on the terminology you use, and new effects may not yet have any\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":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/11\/query.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\/16610","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=16610"}],"version-history":[{"count":4,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16610\/revisions"}],"predecessor-version":[{"id":16617,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16610\/revisions\/16617"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16610"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16610"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16610"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16610"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}