{"id":5368,"date":"2011-11-02T10:10:03","date_gmt":"2011-11-02T10:10:03","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5368"},"modified":"2023-09-16T19:50:25","modified_gmt":"2023-09-16T18:50:25","slug":"spotting-the-unexpected-anomeric-effects-involving-alkenes","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5368","title":{"rendered":"Spotting the unexpected. Anomeric effects involving alkenes?"},"content":{"rendered":"
\n

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 agreed terminology) and a recent excellent review of hyperconjugation<\/a> does not mention it. Here I show how one might provide an answer.<\/p>\n

First, what is an anomeric effect? The diagram below shows the classic anomeric effect in which a donor (an oxygen lone pair) interacts with an acceptor (a C-O bond). The orientation around the single bond shown with a green arrow is crucial; the effect only happens when the donating lone pair is aligned antiperiplanar to the accepting C-O bond, at which point the lengthening<\/strong> of the C-O bond should be maximal (shown as a dashed line below). The blue analogue is the corresponding effect using an alkene as the donor, but retaining the C-O bond as the acceptor.<\/p>\n

\"\"<\/a><\/p>\n

I had previously<\/a>\u00a0addressed this theme by discussing the molecule below. Switching the acceptor from a C-O to a C-cyano bond has the effect of inducing an axial orientation for both cyano groups, a “cyanomeric” effect! Whilst the stronger is undoubtedly the one shown in red, note the blue interaction, that involves an alkene rather than oxygen as donor.<\/p>\n

\"\"<\/a><\/p>\n

One way of providing evidence is a crystallographic search. Here I am using Conquest, the program provided by the Cambridge crystallographic data centre, with the following specification (thanks to Andrew White for helping me frame this search!).<\/p>\n

\"\"<\/a>

The search query<\/p><\/div>\n

    \n
  1. The length of the C-O bond (blue arrow) is defined as a search parameter<\/li>\n
  2. The absolute value of the torsion around the bond (red arrow) is also so defined<\/li>\n
  3. I have restricted the acceptor to C-O bonds (this of course excludes C-CN).<\/li>\n
  4. The C-O acceptor can be enhanced by bearing an electron withdrawing group, which can be e.g.<\/em> carbonyl, phosphate, sulfate, perchlorate etc.<\/li>\n
  5. The alkene donor can be enhanced with donating groups such as oxygen, nitrogen or carbon<\/li>\n
  6. NOT<\/strong> Booleans are applied to restrict the substituents the alkene can carry \u00a0to only sp3<\/sup> carbons (or H) by excluding\u00a0sp2<\/sup><\/em>\u00a0or\u00a0sp<\/em>\u00a0hybridised carbons.\u00a0This is to prevent the substituents from delocalizing the alkene (in effect preventing competition from these substituents), but allowing them to stabilise any induced carbocation resonance by hyperconjugation.<\/li>\n
  7. The C of the C-O is specified as acyclic (to allow the torsion to in theory have any allowed value).<\/li>\n
  8. The search is also restricted to structures with no disorder or other errors, and an R\u00a0factor of < 0.075.<\/li>\n<\/ol>\n
    These specifications can be seen in the first hit obtained:<\/div>\n
    \"\"<\/a>

    A hit<\/p><\/div>\n

    A total of 215 structures are found, and a scatterplot of the C-O bond length version the (abs)C=C-C-O torsion is shown below.<\/p>\n

    \"\"<\/a>

    Scatterplot. Click to view a larger version.<\/p><\/div>\n

    There are two main clusters of hits, those with torsions close to zero, and those with torsions between ~90-120\u00b0. The latter cluster is very clearly shifted to the right of the former, indicating that on average these C-O bond lengths are longer. The red-orange-light green hits (1.46-1.50\u00c5 range) are to be found exclusively in the “antiperiplanar” cluster. One might conclude that statistically, the \u03c0-anomeric effect appears real.\u00a0Of course, there may be many other reasons why the C-O bond is lengthened, and each of the molecules above should be individually inspected to exclude these.<\/p>\n

    This sort of structural search takes only minutes (if you know how to formulate it) and I would certainly encourage you to try it out on your own favourite effect! \u00a0See if the excellent \u00a0and open CrystalEye resource<\/a> gives a similar answer (the Conquest \/CCDC system is commercial, and not open).<\/p>\n

    \n

    H. S. Rzepa, 2011-11-02. URL:http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5368. Accessed: 2011-11-02. (Archived by WebCite\u00ae at http:\/\/www.webcitation.org\/62tOSgnzK<\/a>)<\/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":"

    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 agreed terminology) and a recent […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2,1],"tags":[736,311,737,678,17,733,552,732,734,735],"ppma_author":[2661],"class_list":["post-5368","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-general","tag-andrew","tag-andrew-white","tag-anomeric","tag-chemical-abstracts","tag-conformational-analysis","tag-crystallographic-search","tag-disorder","tag-search-parameter","tag-search-query","tag-structural-search-takes"],"yoast_head":"\nSpotting the unexpected. Anomeric effects involving alkenes? - 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=5368\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Spotting the unexpected. Anomeric effects involving alkenes? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"How one might go about answering the question: do alkenes promote anomeric effects? 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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":745,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=745","url_meta":{"origin":5368,"position":1},"title":"Spotting the unexpected: Anomeric effects","author":"Henry Rzepa","date":"September 18, 2009","format":false,"excerpt":"Chemistry can be very focussed nowadays. This especially applies to target-driven synthesis, where the objective is to make a specified molecule, in perhaps as an original manner as possible. A welcome, but not always essential aspect of such syntheses is the discovery of new chemistry. In this blog, I will\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":"A cyano-substituted cis decalin","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/anomeric-cn.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16468,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468","url_meta":{"origin":5368,"position":2},"title":"The geometries of 5-coordinate compounds of group 14 elements.","author":"Henry Rzepa","date":"May 30, 2016","format":false,"excerpt":"This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry.\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":16696,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16696","url_meta":{"origin":5368,"position":3},"title":"A periodic table for anomeric centres, this time with quantified interactions.","author":"Henry Rzepa","date":"August 8, 2016","format":false,"excerpt":"The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I\u00a0quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:A two-coordinate atom across the series B-O 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":"","src":"","width":0,"height":0},"classes":[]},{"id":16671,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16671","url_meta":{"origin":5368,"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":14508,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508","url_meta":{"origin":5368,"position":5},"title":"A visualization of the anomeric effect from crystal structures.","author":"Henry Rzepa","date":"August 27, 2015","format":false,"excerpt":"The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. 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":[]}],"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\/5368","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=5368"}],"version-history":[{"count":3,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5368\/revisions"}],"predecessor-version":[{"id":26486,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5368\/revisions\/26486"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5368"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5368"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5368"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=5368"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}