{"id":16844,"date":"2016-09-21T15:38:35","date_gmt":"2016-09-21T14:38:35","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16844"},"modified":"2017-07-14T14:03:13","modified_gmt":"2017-07-14T13:03:13","slug":"%cf%83-or-%cf%80-the-ambident-nucleophilic-reactivity-of-imines-crystallographic-and-computational-reality-checks","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16844","title":{"rendered":"\u03c3 or \u03c0? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"16844\">\n<p>Nucleophiles are species\u00a0that seek to react with an electron deficient centre by donating a lone or a \u03c0-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine\u00a0or\u00a0H<sub>2<\/sub>NOH. I <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=7779\">previously discussed<\/a> how for this example, the energetics allow\u00a0the nitrogen lone pair (Lp) to win out over the O Lp. Here, I play a similar game, but this time setting an N<sub>Lp<\/sub> up against a \u03c0-pair.<\/p>\n<p><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/oxaziridine.svg\"><img decoding=\"async\" class=\"aligncenter size-large wp-image-16846\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/oxaziridine.svg\" alt=\"oxaziridine\" width=\"350\" \/><\/a><\/p>\n<p>Before exploring this computationally, \u00a0a reality check using measured crystal structures. Below is the search query used to explore the ability of the imine \u03c0-bond (the more novel or unusual of the two possibilities) to hydrogen bond to a proton as the model electrophile (see <span id=\"cite_ITEM-16844-0\" name=\"citation\"><a href=\"#ITEM-16844-0\">[1]<\/a><\/span> for anther example of using this as a probe).<\/p>\n<p><img decoding=\"async\" class=\"aligncenter size-full wp-image-16865\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/imine1.jpg\" alt=\"imine1\" width=\"450\" \/><\/p>\n<p>DIST1 is the distance from a hydrogen to the mid-point of the C=N bond (set to be in the range 1.8-2.7\u00c5, the latter being shorter than the combined van der Waals radii of the atoms). The torsion is set to |70-110|\u00b0 to restrict the approach of the hydrogen to above or below the\u00a0\u03c0-bond. The usual no errors, no disorder, R &lt; 0.05 and H-positions normalised applies. Some 2501 hits for intermolecular approaches closer than the van der Waals contact are found, with one hot-spot at a distance of 2.65\u00c5 and a torsion of ~100\u00b0. There is of course a continuum between a hydrogen bond and a dispersion attraction, but this plot shows there to be a fair few examples at distances of 2.4\u00c5, a shortening which is normally taken as a hydrogen bond rather than a dispersion mode.\u00a0<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-16866\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/imine2.jpg\" alt=\"imine2\" width=\"450\" height=\"263\" \/><\/p>\n<p>Using a\u00a0simple imine as the nucleophile\u00a0and a peracid as\u00a0electrophile,<span id=\"cite_ITEM-16844-1\" name=\"citation\"><a href=\"#ITEM-16844-1\">[2]<\/a><\/span> \u03c9B97XD\/Def2-TZVPP\/SCRF=dichloromethane calculations (N<sub>lp<\/sub><span id=\"cite_ITEM-16844-2\" name=\"citation\"><a href=\"#ITEM-16844-2\">[3]<\/a><\/span>,N<sub>\u03c0<\/sub><span id=\"cite_ITEM-16844-3\" name=\"citation\"><a href=\"#ITEM-16844-3\">[4]<\/a><\/span>) reveal the N<sub>lp<\/sub> barrier to be <strong><span style=\"color: #ff0000;\">16.2<\/span><\/strong> kcal\/mol lower in free energy (\u0394G<sub>298<\/sub>) than N<sub>\u03c0<\/sub>. The normal explanation is that a Lp is bound only to a single nucleus, whereas a two-centre bonded pair is attracted to two nuclei. The means that the former therefore is more readily &#8220;available&#8221; to donate to an electrophile, by apparently 16.2 kcal\/mol.<\/p>\n<p>The IRC energy profile<span id=\"cite_ITEM-16844-4\" name=\"citation\"><a href=\"#ITEM-16844-4\">[5]<\/a><\/span> for N<sub>lp<\/sub> as a \u03c3-nucleophile is shown below, with a relatively reasonable thermal barrier to reaction. The feature at IRC = 2 is in fact the proton transfer, which occurs only after the transition state has been passed. This behaviour was <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=11065\">noted previously<\/a>\u00a0for the reaction of ethene with peracid,\u00a0as verified experimentally by the measurement of kinetic isotope effects.<\/p>\n<p><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/NE.svg\"><img decoding=\"async\" class=\"aligncenter size-large wp-image-16848\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/NE.svg\" alt=\"ne\" width=\"450\" \/><\/a><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/NG.svg\"><img decoding=\"async\" class=\"aligncenter size-large wp-image-16849\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/NG.svg\" alt=\"ng\" width=\"450\" \/><\/a><\/p>\n<p><img decoding=\"async\" class=\"aligncenter size-full wp-image-16885\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/N1.gif\" alt=\"n1\" width=\"450\" \/><\/p>\n<p>The\u00a0\u03c0-nucleophilic route is shown below.<span id=\"cite_ITEM-16844-5\" name=\"citation\"><a href=\"#ITEM-16844-5\">[6]<\/a><\/span> Note the higher barrier and the greater synchrony between the oxygen transfer and the proton transfer.<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/PiE.svg\"><img decoding=\"async\" class=\"aligncenter size-large wp-image-16851\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/PiE.svg\" alt=\"pie\" width=\"450\" \/><\/a><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/PiG.svg\"><img decoding=\"async\" class=\"aligncenter size-large wp-image-16852\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/PiG.svg\" alt=\"pig\" width=\"450\" \/><\/a><\/p>\n<p><img decoding=\"async\" class=\"aligncenter size-full wp-image-16887\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/pi1.gif\" alt=\"pi1\" width=\"440\" \/><\/p>\n<p>This leaves us with something of a problem. According to the literature,<span id=\"cite_ITEM-16844-1\" name=\"citation\"><a href=\"#ITEM-16844-1\">[2]<\/a><\/span>\u00a0the balance between\u00a0\u03c3 or \u03c0 is very even for the reaction between a peracid and an imine. For an aryl substituted imine, the proportion of the two products changes from 0% N (nitrone) and 100% \u03c0\u00a0(oxaziridine) to 78% N and 22% \u03c0 simply by changing the nature of the substituent. To achieve what is often referred to as 100% selectivity (normally understood as the minor isomer being &lt;1% of the formed products) takes a free energy difference of ~2.7 kcal\/mol (in fact ~RT ln 100\/1), and a complete inversion is therefore ~5.4 kcal\/mol. The computed difference of 16.2 kcal\/mol is far too large to achieve such an inversion (substituent effects are rarely if ever of this magnitude). When faced with such a mismatch between experiment and computation, the explanation is normally\u00a0because the modelled mechanism is the wrong one. So in this case, time to hunt for an alternative way of forming the oxaziridine.\u00a0If I find a solution, I will <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16902\">update this post<\/a>.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-16844-0\">H.S. Rzepa, \"Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases\", <i>Journal of Chemical Education<\/i>, vol. 93, pp. 550-554, 2015. <a href=\"https:\/\/doi.org\/10.1021\/acs.jchemed.5b00346\">https:\/\/doi.org\/10.1021\/acs.jchemed.5b00346<\/a>\n\n<\/li>\n<li id=\"ITEM-16844-1\">D.R. Boyd, P.B. Coulter, N.D. Sharma, W. Jennings, and V.E. Wilson, \"Normal, abnormal and pseudo-abnormal reaction pathways for the imine-peroxyacid reaction\", <i>Tetrahedron Letters<\/i>, vol. 26, pp. 1673-1676, 1985. <a href=\"https:\/\/doi.org\/10.1016\/s0040-4039(00)98582-4\">https:\/\/doi.org\/10.1016\/s0040-4039(00)98582-4<\/a>\n\n<\/li>\n<li id=\"ITEM-16844-2\">H.S. Rzepa, \"C 3 H 7 N 1 O 3\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/ch\/195458\">https:\/\/doi.org\/10.14469\/ch\/195458<\/a>\n\n<\/li>\n<li id=\"ITEM-16844-4\">H. Rzepa, \"Imine + peracetic acid,N attack IRC\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/1658\">https:\/\/doi.org\/10.14469\/hpc\/1658<\/a>\n\n<\/li>\n<li id=\"ITEM-16844-5\">H. Rzepa, \"Imine + peracetic acid, pi attack IRC\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/1659\">https:\/\/doi.org\/10.14469\/hpc\/1659<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 16844 -->","protected":false},"excerpt":{"rendered":"<p>Nucleophiles are species\u00a0that seek to react with an electron deficient centre by donating a lone or a \u03c0-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine\u00a0or\u00a0H2NOH. I previously discussed how for this example, the energetics allow\u00a0the nitrogen lone pair [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":true,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_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},"jetpack_post_was_ever_published":false},"categories":[1745,1086],"tags":[],"ppma_author":[2661],"class_list":["post-16844","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-reaction-mechanism-2"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>\u03c3 or \u03c0? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks. - 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=16844\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u03c3 or \u03c0? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Nucleophiles are species\u00a0that seek to react with an electron deficient centre by donating a lone or a \u03c0-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine\u00a0or\u00a0H2NOH. I previously discussed how for this example, the energetics allow\u00a0the nitrogen lone pair [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16844\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-09-21T14:38:35+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-07-14T13:03:13+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/oxaziridine.svg\" \/>\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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"\u03c3 or \u03c0? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks. - 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=16844","og_locale":"en_GB","og_type":"article","og_title":"\u03c3 or \u03c0? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks. - Henry Rzepa&#039;s Blog","og_description":"Nucleophiles are species\u00a0that seek to react with an electron deficient centre by donating a lone or a \u03c0-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine\u00a0or\u00a0H2NOH. I previously discussed how for this example, the energetics allow\u00a0the nitrogen lone pair [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16844","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2016-09-21T14:38:35+00:00","article_modified_time":"2017-07-14T13:03:13+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/oxaziridine.svg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16844#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16844"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"\u03c3 or \u03c0? 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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":9572,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9572","url_meta":{"origin":16844,"position":2},"title":"A to-and-fro of electrons operating in s-cis esters.","author":"Henry Rzepa","date":"February 21, 2013","format":false,"excerpt":"I conclude my exploration of conformational preferences by taking a look at esters. As before, I start with a search definition, the ester being restricted to one bearing only sp3 carbon centers. The result of such a search is pretty clear-cut; they all exist in just one conformation, the s-cis,\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":"s-cis-ester-torsion-search","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/s-cis-ester-torsion-search.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":1278,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1278","url_meta":{"origin":16844,"position":3},"title":"The nature of the C\u2261S triple bond: part 3.","author":"Henry Rzepa","date":"December 6, 2009","format":false,"excerpt":"In the previous two posts, a strategy for tuning the nature of the CS bond in the molecule HO-S\u2261C-H was developed, based largely on the lone pair of electrons identified on the carbon atom. By replacing the HO group by one with greater \u03c3-electron withdrawing propensity, the stereo-electronic effect between\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The H2BSCH molecule. Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/12\/CSBH2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24067,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24067","url_meta":{"origin":16844,"position":4},"title":"Dimerisation of cyclopropenylidene: what are the correct &#8220;curly arrows&#8221; for this process?","author":"Henry Rzepa","date":"July 21, 2021","format":false,"excerpt":"In another post, a discussion arose about whether it might be possible to trap\u00a0cyclopropenylidene to form a small molecule with a large dipole moment. Doing so assumes that cyclopropenylidene has a sufficiently long lifetime to so react, before it does so with itself to e.g. dimerise. That dimerisation has an\u2026","rel":"","context":"In &quot;Curly arrows&quot;","block_context":{"text":"Curly arrows","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2327"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":9056,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056","url_meta":{"origin":16844,"position":5},"title":"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems.","author":"Henry Rzepa","date":"January 8, 2013","format":false,"excerpt":"In this post, I looked at some hydrogen bonds formed by interaction of a\u00a0\u03c0-system with an acidic hydrogen. Unlike normal lone pair donors, \u03c0-systems can involve more than two electrons, most commonly four or six. Here I look at examples of both these higher-order donors. FIMNEU The NCI surface for\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":"FIMNEU.  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