{"id":16361,"date":"2016-05-11T13:00:50","date_gmt":"2016-05-11T12:00:50","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16361"},"modified":"2016-06-26T08:24:35","modified_gmt":"2016-06-26T07:24:35","slug":"what-is-the-approach-trajectory-of-enhanced-super-nucleophiles-towards-a-carbonyl-group","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361","title":{"rendered":"What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group?"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"16361\">\n<p>\n\tI have<a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14016\" target=\"_blank\"> previously commented<\/a> on the B&uuml;rgi&ndash;Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R<sub>2<\/sub>N-NR<sub>2<\/sub>) are supposed to have enhanced reactivity<span id=\"cite_ITEM-16361-0\" name=\"citation\"><a href=\"#ITEM-16361-0\">[1]<\/a><\/span> due to what might be described as&nbsp;buttressing of adjacent lone pairs. Here&nbsp;I focus in on how this might manifest by performing searches of the Cambridge structural database for intermolecular (non-bonded) interactions between X-Y&nbsp;nucleophiles (X,Y= N,O,S) and carbonyl compounds OC(NM)<sub>2<\/sub>.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/sq.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tThe search query<span id=\"cite_ITEM-16361-1\" name=\"citation\"><a href=\"#ITEM-16361-1\">[2]<\/a><\/span> is shown above and involves plotting the distance from the nucleophilic atom (N above) to the carbon of the carbonyl group. The carbon is defined as having 3-coordination, one of which is O=C and two non-metal attachments. The torsion is constrained to values of |70-110|&deg; to ensure that the approach of the nucleophile is approximately perpendicular to the plane of the carbonyl in order to overlap with the&nbsp;&pi;*-orbital as electrophile. The pairwise sums of van&nbsp;der&nbsp;Waals radii are NC, 3.25; OC, 3.22 and SC, 3.5&Aring; and the plots show all contacts shorter than these.&nbsp;The results of the searches are shown below.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/nn-c_o.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/oo-c_o.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/ss-c_o.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tThe general observation is that the red hotspots do tend to come at trajectory angles of &lt;100&deg;&nbsp;and many are &lt;90&deg; such as the X=Y=N or X=Y=S examples. Given that the original&nbsp;B&uuml;rgi&ndash;Dunitz hypothesis (actually based on a small number of molecules synthesized for the purpose) proposed rather larger angles (105&plusmn;5&deg;) corresponding to optimum alignment of the nucleophile with the carbonyl &pi;*-orbital, we&nbsp;might speculate whether the use of enhanced nucleophiles is the reason for the apparent decrease in the angle. And if so, what the underlying reasons would be.\n<\/p>\n<p>\n\tI also cannot help but observe&nbsp;that the term <span style=\"color: #ff0000;\"><strong>supernucleophile<\/strong><\/span> is quite rare in the literature;&nbsp;SciFinder gives only 45 hits, but most are about neither hydrazines nor peroxides. There are also some unusual nucleophile varieties such as Cob(I)alamin<span id=\"cite_ITEM-16361-2\" name=\"citation\"><a href=\"#ITEM-16361-2\">[3]<\/a><\/span>, of which there are probably insufficient examples to reflect in the crystal structure statistics shown above. Given the interest in <a href=\"https:\/\/en.wikipedia.org\/wiki\/Superbase\">superbases<\/a>, the relative lack of examples of unusual supernucleophiles seems surprising.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-16361-0\">G. Klopman, K. Tsuda, J. Louis, and R. Davis, \"Supernucleophiles\u2014I\", <i>Tetrahedron<\/i>, vol. 26, pp. 4549-4554, 1970. <a href=\"https:\/\/doi.org\/10.1016\/s0040-4020(01)93101-1\">https:\/\/doi.org\/10.1016\/s0040-4020(01)93101-1<\/a>\n\n<\/li>\n<li id=\"ITEM-16361-1\">H. Rzepa, \"Crystal structure search using enhanced nucleophiles\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/487\">https:\/\/doi.org\/10.14469\/hpc\/487<\/a>\n\n<\/li>\n<li id=\"ITEM-16361-2\">K.P. Jensen, \"Electronic Structure of Cob(I)alamin:\u2009 The Story of an Unusual Nucleophile\", <i>The Journal of Physical Chemistry B<\/i>, vol. 109, pp. 10505-10512, 2005. <a href=\"https:\/\/doi.org\/10.1021\/jp050802m\">https:\/\/doi.org\/10.1021\/jp050802m<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 16361 -->","protected":false},"excerpt":{"rendered":"<p>I have previously commented on the B&uuml;rgi&ndash;Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity due to what might be described as&nbsp;buttressing of adjacent lone pairs. Here&nbsp;I focus in on [&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":[1623,1430,1427,1444,1756,1796,1412,241,1797,1794,1442,734,1795],"ppma_author":[2661],"class_list":["post-16361","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-bases","tag-burgi-dunitz-angle","tag-carbonyl","tag-electrophile","tag-ester","tag-flippin-lodge-angle","tag-functional-groups","tag-hydrazine","tag-non-metal-attachments","tag-nucleophile","tag-physical-organic-chemistry","tag-search-query","tag-superbase"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group? - 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=16361\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group? - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"I have previously commented on the B&uuml;rgi&ndash;Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity due to what might be described as&nbsp;buttressing of adjacent lone pairs. Here&nbsp;I focus in on [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-05-11T12:00:50+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-06-26T07:24:35+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/sq.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":"What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group? - 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=16361","og_locale":"en_GB","og_type":"article","og_title":"What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group? - Henry Rzepa&#039;s Blog","og_description":"I have previously commented on the B&uuml;rgi&ndash;Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. 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Here&nbsp;I focus in on [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2016-05-11T12:00:50+00:00","article_modified_time":"2016-06-26T07:24:35+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/sq.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group?","datePublished":"2016-05-11T12:00:50+00:00","dateModified":"2016-06-26T07:24:35+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361"},"wordCount":409,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/sq.jpg","keywords":["Bases","B\u00fcrgi\u2013Dunitz angle","Carbonyl","Electrophile","Ester","Flippin\u2013Lodge angle","Functional groups","hydrazine","non-metal attachments","Nucleophile","Physical organic chemistry","search query","Superbase"],"articleSection":["Chemical IT","crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16361","name":"What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group? 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Its value obviously depends on the exact system, but is generally taken to be in the range 105-107\u00b0. A very\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":16361,"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":26523,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26523","url_meta":{"origin":16361,"position":2},"title":"More examples of &#8220;double-headed&#8221; curly arrows: S and C Nucleophiles attacking acetyl chloride","author":"Henry Rzepa","date":"October 12, 2023","format":false,"excerpt":"In an earlier post on this topic,\u2021 I described how the curly-arrows describing the mechanism of a nucleophilic addition at a carbonyl group choreograph in two distinct ways, as seen in red or blue below. The arrows in red can be described as firstly addition to the carbonyl group to\u2026","rel":"","context":"In \"Interesting chemistry\"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=interesting-chemistry"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":14161,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161","url_meta":{"origin":16361,"position":3},"title":"The formation of tetrahedral intermediates.","author":"Henry Rzepa","date":"June 12, 2015","format":false,"excerpt":"In the preceding post, I discussed\u00a0the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly\u00a0pointed out\u00a0on this blog that his was a mixed-phase reaction, and that mechanistic comparison\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":13688,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13688","url_meta":{"origin":16361,"position":4},"title":"Mechanism of the Lithal (LAH) reduction of cinnamaldehyde.","author":"Henry Rzepa","date":"April 1, 2015","format":false,"excerpt":"The reduction of cinnamaldehyde by lithium aluminium hydride (LAH) was reported in a classic series of experiments,, dating from 1947-8. The reaction was first introduced into the organic chemistry laboratories here at Imperial College decades ago, vanished for a short period, and has recently been reintroduced again.\u2021 The experiment is\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":8216,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8216","url_meta":{"origin":16361,"position":5},"title":"Secrets revealed for conjugate addition to cyclohexenone using a Cu-alkyl reagent.","author":"Henry Rzepa","date":"November 4, 2012","format":false,"excerpt":"The text books say that cyclohexenone A will react with a Grignard reagent by delivery of an alkyl (anion) to the carbon of the carbonyl (1,2-addition) but if dimethyl lithium cuprate is used, a conjugate 1,4-addition proceeds, to give the product B shown below. The standard explanation is that the\u2026","rel":"","context":"In \"metal\"","block_context":{"text":"metal","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=metal"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/11\/4.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\/16361","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=16361"}],"version-history":[{"count":22,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16361\/revisions"}],"predecessor-version":[{"id":16389,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16361\/revisions\/16389"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16361"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16361"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16361"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16361"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}