{"id":14537,"date":"2015-09-05T09:32:09","date_gmt":"2015-09-05T08:32:09","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14537"},"modified":"2023-09-17T07:23:23","modified_gmt":"2023-09-17T06:23:23","slug":"%cf%80-resonance-in-amides-a-crystallographic-reality-check","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14537","title":{"rendered":"\u03c0-Resonance in amides: a crystallographic reality check."},"content":{"rendered":"
\n

\n\tThe π-resonance in amides famously helped Pauling to his propos<\/a>al of a helical structure for proteins. Here I explore some geometric properties of amides related to the C-N bond and the torsions about it.\n<\/p>\n

\n\t\"Scheme\"\n<\/p>\n

\n\tThe key aspect of amides is that a lone pair of electrons on the nitrogen can conjugate with the C=O carbonyl only if the lone pair orbital is parallel to the C-O π-system. We can define this with the O=C-N-R torsion angle (and equate 0 or 180° with the p-orbitals being parallel). In the above definition, each R can be either 4-coordinate C (to avoid alternative conjugations) or H and the C-N bond is specified as being cyclic. As usual the R-factor is < 5%, no errors, no disorder.\n<\/p>\n

\n\tFirst, the C-N torsion, which adopts values of either 0 or 180°. Notice that whilst the anti<\/em> R-group shows no more than about 20° deviation from 180°, it does have a small tail tending towards longer C-N distances of >1.4Å. The hotspot is for the syn<\/em> R-group.  Here there is a strong trend that as the dihedral deviates from 0° the C-N bond very clearly elongates. As the π-π overlap decreases, the bond elongates from the hot spot value of ~1.34Å to 1.41Å at 50°. The greater propensity of the syn<\/em>-R to twist may be because it incurs more steric hindrance or perhaps because we have defined the C-N bond to be part of a cycle.\n<\/p>\n

\n\t\"Scheme\"\n<\/p>\n

\n\tNext, we plot the C-N distance against the torsion R-N-C-R', which defines how planar the nitrogen is. A value of 180° is planar and the hot-spot is here. But as the planarity decreases down to almost tetrahedral (110°) the C-N bond elongates to  1.41Å. Notice one rather intriguing aspect;  from 180° to 160° or so, there is little response from the  C-N bond, but the elongation really accelerates from 140° to 110°. A little twisting hardly affects the π-π overlap, but it really starts to matter for twists of >50°.\n<\/p>\n

\n\t\"Scheme\"\n<\/p>\n

\n\tFinally a plot of the C-N vs the C-O distances. As the C-N increases, the C-O contracts, this being a nice summary of the π resonance in amides. \n<\/p>\n

\n\t\"Scheme\"\n<\/p>\n

\n\tWe have not seen any surprises, but this statistical exploration of crystal structures at least puts some numbers on the changes in bond lengths as a result of conjugative resonance.\n<\/p>\n

\n

Acknowledgments<\/h4>\n

This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

The π-resonance in amides famously helped Pauling to his proposal of a helical structure for proteins. Here I explore some geometric properties of amides related to the C-N bond and the torsions about it. The key aspect of amides is that a lone pair of electrons on the nitrogen can conjugate with the C=O carbonyl only […]<\/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":[2,1745],"tags":[1556,557,1558,1442,1559],"ppma_author":[2661],"class_list":["post-14537","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-amide","tag-chemical-bonding","tag-conjugated-system","tag-physical-organic-chemistry","tag-resonance"],"yoast_head":"\n\u03c0-Resonance in amides: a crystallographic reality check. - 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=14537\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u03c0-Resonance in amides: a crystallographic reality check. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The π-resonance in amides famously helped Pauling to his proposal of a helical structure for proteins. 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The key aspect of amides is that a lone pair of electrons on the nitrogen can conjugate with the C=O carbonyl only […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14537\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-09-05T08:32:09+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-17T06:23:23+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/Amide-def.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":"\u03c0-Resonance in amides: a crystallographic reality check. - 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=14537","og_locale":"en_GB","og_type":"article","og_title":"\u03c0-Resonance in amides: a crystallographic reality check. - Henry Rzepa's Blog","og_description":"The π-resonance in amides famously helped Pauling to his proposal of a helical structure for proteins. Here I explore some geometric properties of amides related to the C-N bond and the torsions about it. 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Here I compare the analysis with that for the closely related thioamides. Here is the torsional analysis around the C-N bond. The \"diff\" (difference) is that almost all the hits are concentrated into angles of 0\u00b0 or 180\u00b0; the twist about the\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":12678,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12678","url_meta":{"origin":14537,"position":1},"title":"Amides and inverting the electronics of the B\u00fcrgi\u2013Dunitz trajectory.","author":"Henry Rzepa","date":"June 26, 2014","format":false,"excerpt":"The B\u00fcrgi\u2013Dunitz angle describes the trajectory of an approaching nucleophile towards the carbon atom of a carbonyl group. A colleague recently came to my office to ask about the inverse, that is what angle would an electrophile approach (an amide)? Thus it might approach either syn or\u00a0anti\u00a0with respect to 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":"","src":"","width":0,"height":0},"classes":[]},{"id":11954,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11954","url_meta":{"origin":14537,"position":2},"title":"A congruence of concepts: conformations, configurations, amides and enzymes","author":"Henry Rzepa","date":"February 9, 2014","format":false,"excerpt":"This is the time of year when I deliver two back-2-back lecture courses, and yes I do update and revise the content! I am always on the look-out for nice new examples that illustrate how concepts and patterns in chemistry can be joined up to tell a good story. My\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":9459,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9459","url_meta":{"origin":14537,"position":3},"title":"The conformational preference of s-cis amides.","author":"Henry Rzepa","date":"February 10, 2013","format":false,"excerpt":"Amides with an H-N group are a component of the peptide linkage\u00a0(O=C-NH). Here I ask what the conformation (it could also be called a configuration) about the C-N bond is. 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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\/14537","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=14537"}],"version-history":[{"count":9,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14537\/revisions"}],"predecessor-version":[{"id":26500,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14537\/revisions\/26500"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14537"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14537"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14537"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14537"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}