{"id":9360,"date":"2013-02-03T08:06:23","date_gmt":"2013-02-03T08:06:23","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=9360"},"modified":"2023-09-16T19:43:37","modified_gmt":"2023-09-16T18:43:37","slug":"%cf%83-%cf%80-conjugation-seeking-evidence-by-a-survey-of-crystal-structures","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9360","title":{"rendered":"\u03c3-\u03c0-Conjugation: seeking evidence by a survey of crystal structures."},"content":{"rendered":"
\n

\n\tThe electronic interaction between a single bond and an adjacent double bond is often called σ-π-conjugation (an older term for this is hyperconjugation), and the effect is often used to e.g.<\/em> explain why more highly substituted carbocations are more stable than less substituted ones. This conjugation is more subtle in neutral molecules, but following my use of crystal structures to explore the so-called gauche effect<\/a> (which originates from σ-σ-conjugation), I thought I would have a go here at seeing what the crystallographic evidence actually is for the σ-π-type.\n<\/p>\n

\n\t\"sigma-pi-conjugation\"<\/a>\n<\/p>\n

\n\tThe basic two molecules are shown above; in effect propene 1<\/strong> and butene 2<\/strong>. The latter was in fact the topic of another post<\/a>, in which I attempted to show that the close H…H contact in cis<\/em>-butene (2.1Å) was in effect an unwelcome consequence of the σ-π-conjugation of any of the four "outward leaning" C-H bonds of the methyl groups acting as donors (red-blue below) overlapping with the similarly "outward leaning" π* orbital of the alkene (purple-orange below; blue and purple overlap positively).\n<\/p>\n

\"C-H\/alkene

NBO orbitals for C-H\/alkene interaction. Click for 3D.<\/p><\/div>\n

\n\tSo how general might this be? To find out, I performed the following search on the Cambridge crystal database: \"cis-butene-search\"<\/a>\n<\/p>\n

    \n
  1. \n\t\tThe search defines an alkene, bearing two cis-substituents each with at least one C-H bond. The substituents are both sp3<\/sup> carbon, and the attachment bond to the alkene is defined as acyclic\n\t<\/li>\n
  2. \n\t\tThe H…H distance uses normalised terminal hydrogen positions (to try to correct for the normally over-short C-H bond lengths found by X-ray).\n\t<\/li>\n
  3. \n\t\tOther constraints were R factor < 0.05, no disorder, no errors and (perhaps most importantly) T < 150K to try to reduce thermal libration.\n\t<\/li>\n<\/ol>\n

    \n\tI should qualify all of this by reminding that hydrogen positions in crystal structures are notoriously prone to errors. Nevertheless, with 624 hits using the above search, one might hope for statistical significance of a real effect.\n<\/p>\n

    \"Search

    Search result for close H…H contacts in cis-butenes.<\/p><\/div>\n

    \n\tFor this sample, the most frequent H…H distance emerged as 2.1Å. This can only result from having the C-H bonds lie coplanar with the C=C alkene, as is shown above. The value is also remarkably close to the H…H distance for cis<\/em>-butene itself (both computationally and as determined using electron diffraction). This does I feel provide a strong indication that σ-π-conjugation is manifesting in these systems.\n<\/p>\n

    \n\tRe-defining the search for propenes 1<\/strong> as above gives 1656 hits, with a maximum in the distribution at 2.35Å corresponding to a syn<\/em>-orientation of the C=C and the C-H bonds. The smaller maximum at about 2.75Å arises from a gauche-<\/em>orientation between the C=C and C-H (in effect you have to halve this number, since there are twice as many possibilities for this to occur than for the syn<\/em>). The "inward leaning" gauche C-H bond overlaps less well with the "outward leaning" π* orbital of the alkene.\n<\/p>\n

    \"Propene.\"

    Search result for close H…H contacts in propenes.<\/p><\/div>\n

    \n\tThese aspects are perhaps better seen in the orbital overlaps shown below.\n<\/p>\n

    \"Click

    Click for 3D.<\/p><\/div>\n

    \n\tI will follow-up this theme with esters and amides next.\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 electronic interaction between a single bond and an adjacent double bond is often called σ-π-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 neutral molecules, but following my […]<\/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":[1745,4],"tags":[992,144,17,373,42],"ppma_author":[2661],"class_list":["post-9360","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry","tag-above-search","tag-cambridge","tag-conformational-analysis","tag-tutorial-material","tag-x-ray"],"yoast_head":"\n\u03c3-\u03c0-Conjugation: seeking evidence by a survey of crystal structures. - 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=9360\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u03c3-\u03c0-Conjugation: seeking evidence by a survey of crystal structures. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The electronic interaction between a single bond and an adjacent double bond is often called σ-π-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. 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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 "Interesting chemistry"","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":11421,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11421","url_meta":{"origin":9360,"position":1},"title":"Six vs ten aromatic electrons?","author":"Henry Rzepa","date":"October 20, 2013","format":false,"excerpt":"Homoaromaticity is a special case of\u00a0aromaticity\u00a0in which\u00a0\u03c0-conjugation\u00a0is interrupted by a single sp3\u00a0hybridized\u00a0carbon atom (it is sometimes referred to as a suspended \u03c0-bond with no underlying \u03c3-foundation).\u00a0But consider the carbene shown below. This example comes from a recently published article which was highlighted on Steve Bachrach's blog. Here aromaticity has resulted\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":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/10\/B10-sigma.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17205,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17205","url_meta":{"origin":9360,"position":2},"title":"Molecules of the year? The most polar neutral compound synthesized…","author":"Henry Rzepa","date":"December 18, 2016","format":false,"excerpt":"This, the fourth candidate provided by C&EN for a vote for the molecule of the year\u00a0as discussed here,\u00a0lays claim to the World's most polar neutral molecule (system 1 shown below). Here I explore\u00a0a strategy for extending that record. The claim for 1 (3 in\u00a0) is on the basis of its\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":"","width":0,"height":0},"classes":[]},{"id":11757,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11757","url_meta":{"origin":9360,"position":3},"title":"Does forming a Wheland intermediate disrupt all aromaticity?","author":"Henry Rzepa","date":"December 6, 2013","format":false,"excerpt":"Text books will announce that during aromatic electrophilic substitution, aromaticity is lost by the formation of a Wheland intermediate (and regained by eliminating a proton). Is that entirely true? I will start by considering the simplest of all such intermediates, the NMR of which was first reported by Olah and\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":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/12\/wheland-NNM.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24769,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24769","url_meta":{"origin":9360,"position":4},"title":"An unusually small (doubly) aromatic molecule: C4.","author":"Henry Rzepa","date":"March 15, 2022","format":false,"excerpt":"When you talk \u03c0-aromaticity, benzene is the first molecule that springs to mind.\u00a0But there are smaller molecules that can carry this property; cyclopropenylidene (five atoms) is the smallest in terms of atom count I could think of until now, apart that is from H3+ which is the smallest possible molecule\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":23777,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23777","url_meta":{"origin":9360,"position":5},"title":"A suggestion for a molecule with a M\u2a78C quadruple bond with trigonal metal coordination.","author":"Henry Rzepa","date":"May 13, 2021","format":false,"excerpt":"The proposed identification of molecules with potential metal to carbon quadruple bonds, in which the metal exhibits trigonal bipyramidal coordination rather than the tetrahedral modes which have been proposed in the literature,, leads on to asking whether simple trigonal coordination at the metal can also sustain this theme? The rational\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":"","width":0,"height":0},"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\/9360","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=9360"}],"version-history":[{"count":22,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9360\/revisions"}],"predecessor-version":[{"id":26478,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9360\/revisions\/26478"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9360"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9360"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9360"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=9360"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}