{"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":"2015-09-05T09:32:09","modified_gmt":"2015-09-05T08:32:09","slug":"%cf%80-resonance-in-amides-a-crystallographic-reality-check","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/blog\/?p=14537","title":{"rendered":"\u03c0-Resonance in amides: a crystallographic reality check."},"content":{"rendered":"
\n

The \u03c0-resonance in amides famously helped Pauling to his propos<\/a>al\u00a0of a helical structure for proteins. Here I explore some geometric properties of amides related to the C-N bond and the torsions about it.<\/p>\n

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

The key aspect of amides is that a lone pair of electrons on the nitrogen can conjugate with the C=O carbonyl only if the\u00a0lone pair orbital is parallel to the C-O \u03c0-system. We can define this with the O=C-N-R torsion angle (and equate 0 or 180\u00b0 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.<\/p>\n

First, the C-N torsion, which adopts values of either 0 or 180\u00b0. Notice that whilst the anti<\/em> R-group shows no more than about 20\u00b0 deviation from 180\u00b0, it does have a small tail tending towards longer C-N distances of >1.4\u00c5. The hotspot is for the syn<\/em> R-group. \u00a0Here there is a strong trend that as the dihedral deviates from\u00a00\u00b0 the C-N bond very clearly elongates. As the\u00a0\u03c0-\u03c0 overlap decreases, the bond elongates from the hot spot value of ~1.34\u00c5 to 1.41\u00c5 at 50\u00b0. The greater propensity of the syn<\/em>-R to twist may be because it incurs more steric hindrance or\u00a0perhaps\u00a0because we have defined the C-N bond to be part of a cycle.<\/p>\n

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

Next, we plot the C-N distance against the torsion R-N-C-R’, which defines how planar the nitrogen is. A value of\u00a0180\u00b0 is planar and the hot-spot is here. But as the planarity decreases down to almost tetrahedral (110\u00b0) the C-N bond elongates to \u00a01.41\u00c5. Notice one rather intriguing aspect; \u00a0from\u00a0180\u00b0 to\u00a0160\u00b0 or so, there is little response from the \u00a0C-N bond, but the elongation really accelerates from\u00a0140\u00b0 to\u00a0110\u00b0. A little twisting hardly affects the\u00a0\u03c0-\u03c0 overlap, but\u00a0it really starts to matter for twists of >50\u00b0.<\/p>\n

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

Finally a plot of the C-N vs the C-O distances. As the C-N increases, the C-O contracts, this being\u00a0a nice summary of the\u00a0\u03c0 resonance in amides.\u00a0<\/p>\n

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

We 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.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

The \u03c0-resonance in amides famously helped Pauling to his proposal\u00a0of 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,"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":[3,1754],"tags":[1557,510,1569,1497,1604],"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"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p1gPyz-3Mt","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14537","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=14537"}],"version-history":[{"count":0,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14537\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14537"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14537"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14537"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}