{"id":14543,"date":"2015-09-05T11:17:55","date_gmt":"2015-09-05T10:17:55","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14543"},"modified":"2023-09-17T07:13:29","modified_gmt":"2023-09-17T06:13:29","slug":"%cf%80-resonance-in-thioamides-a-crystallographic-diff-with-amides","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14543","title":{"rendered":"\u03c0-Resonance in thioamides: a crystallographic &#8220;diff&#8221; with amides."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"14543\">\n<p>The\u00a0previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides.<\/p>\n<p><img decoding=\"async\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/SAmide-def.jpg\" alt=\"Scheme\" width=\"400\" \/><\/p>\n<p>Here is the torsional analysis around the C-N bond. The &#8220;diff&#8221; (difference) is that almost all the hits are concentrated into angles of 0\u00b0 or 180\u00b0; the twist about the C-N bond\u00a0from co-planarity is much less if S is present. This is normally explained in terms of Sp<sub>\u03c0<\/sub>-Cp<sub>\u03c0<\/sub> overlaps being less favourable than Op<sub>\u03c0<\/sub>-Cp<sub>\u03c0<\/sub> ones owing to the mismatch in the size of the atomic orbital for S and C. Hence the resonance which reduces the C=S double bond character in favour of greater C=N character is enhanced\u00a0compared to O.<\/p>\n<p><img decoding=\"async\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/SAmide-torsions1.jpg\" alt=\"Scheme\" width=\"440\" \/><\/p>\n<p>A consequence is that the nitrogen atom is less easily deformed from planarity in a thioamide. Notice also that at the hotspot, the C=N distance is ~1.32\u00c5 compared to 1.34\u00c5 for a regular amide.<\/p>\n<p><img decoding=\"async\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/SAmide-torsions2.jpg\" alt=\"Scheme\" width=\"440\" \/><\/p>\n<p>This emerges from the plot below as well; the range of values for the C-N bond is reduced compared to amides, but the diagonal trend that as the C=N bond gets longer so the C-S gets shorter is still seen.<\/p>\n<p><img decoding=\"async\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/SAmide-torsions3.jpg\" alt=\"Scheme\" width=\"440\" \/><\/p>\n<p>All these trends are described qualitatively in most text books of organic chemistry, but one never sees statistical evidence for them. And it truly only takes 5-10 minutes to produce.<\/p>\n<hr \/>\n<h4>Acknowledgments<\/h4>\n<p>This post has been cross-posted in PDF format at <a href=\"https:\/\/doi.org\/10.15200\/winn.144212.25425\" rel=\"noopener\" target=\"_blank\">Authorea<\/a>.<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 14543 -->","protected":false},"excerpt":{"rendered":"<p>The\u00a0previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides. Here is the torsional analysis around the C-N bond. The &#8220;diff&#8221; (difference) is that almost all the hits are concentrated into angles of 0\u00b0 or 180\u00b0; the twist about the C-N bond\u00a0from co-planarity is much [&hellip;]<\/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":[1556,1412,1557],"ppma_author":[2661],"class_list":["post-14543","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-amide","tag-functional-groups","tag-thioamide"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>\u03c0-Resonance in thioamides: a crystallographic &quot;diff&quot; with amides. - Henry Rzepa&#039;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=14543\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u03c0-Resonance in thioamides: a crystallographic &quot;diff&quot; with amides. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The\u00a0previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides. Here is the torsional analysis around the C-N bond. The &#8220;diff&#8221; (difference) is that almost all the hits are concentrated into angles of 0\u00b0 or 180\u00b0; the twist about the C-N bond\u00a0from co-planarity is much [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14543\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-09-05T10:17:55+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-17T06:13:29+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/SAmide-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=\"1 minute\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"\u03c0-Resonance in thioamides: a crystallographic \"diff\" with amides. - Henry Rzepa&#039;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=14543","og_locale":"en_GB","og_type":"article","og_title":"\u03c0-Resonance in thioamides: a crystallographic \"diff\" with amides. - Henry Rzepa&#039;s Blog","og_description":"The\u00a0previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides. Here is the torsional analysis around the C-N bond. The &#8220;diff&#8221; (difference) is that almost all the hits are concentrated into angles of 0\u00b0 or 180\u00b0; the twist about the C-N bond\u00a0from co-planarity is much [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14543","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2015-09-05T10:17:55+00:00","article_modified_time":"2023-09-17T06:13:29+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/SAmide-def.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14543#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14543"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"\u03c0-Resonance in thioamides: a crystallographic &#8220;diff&#8221; 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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\u2026","rel":"","context":"In &quot;Chemical IT&quot;","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":14543,"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 &quot;crystal_structure_mining&quot;","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":16758,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16758","url_meta":{"origin":14543,"position":2},"title":"What&#8217;s in a name? Carbenes:  a reality check.","author":"Henry Rzepa","date":"September 11, 2016","format":false,"excerpt":"To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","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":9360,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9360","url_meta":{"origin":14543,"position":3},"title":"\u03c3-\u03c0-Conjugation: seeking evidence by a survey of crystal structures.","author":"Henry Rzepa","date":"February 3, 2013","format":false,"excerpt":"The electronic interaction between a single bond and an adjacent double bond is often called \u03c3-\u03c0-conjugation (an older term for this is hyperconjugation), and the effect is often used to e.g. explain why more highly substituted carbocations are more stable than less substituted ones. This conjugation is more subtle in\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"C-H\/alkene interaction. Click for  3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/cis-butene-orbitals.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":9186,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9186","url_meta":{"origin":14543,"position":4},"title":"The \u03c0-complex in the benzidine rearrangement: a molecular orbital analysis.","author":"Henry Rzepa","date":"January 18, 2013","format":false,"excerpt":"Michael Dewar famously implicated a so-called\u00a0\u03c0-complex in the benzidine rearrangement, back in the days when quantum mechanical calculations could not yet provide a quantitatively accurate reality check. Because this\u00a0\u03c0-complex actually remains a relatively unusual species to encounter in day-to-day chemistry, I thought I would try to show in a simple\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":1856,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1856","url_meta":{"origin":14543,"position":5},"title":"Conformational analysis of biphenyls: an upside-down view","author":"Henry Rzepa","date":"April 2, 2010","format":false,"excerpt":"One of the (not a few) pleasures of working in a university is the occasional opportunity that arises to give a new lecture course to students. New is not quite the correct word, since the topic I have acquired is Conformational analysis. The original course at Imperial College was delivered\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/04\/biphenyl-1.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\/14543","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=14543"}],"version-history":[{"count":4,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14543\/revisions"}],"predecessor-version":[{"id":26490,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14543\/revisions\/26490"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14543"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14543"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14543"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14543"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}