{"id":18822,"date":"2017-09-21T07:55:06","date_gmt":"2017-09-21T06:55:06","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18822"},"modified":"2017-09-22T10:18:05","modified_gmt":"2017-09-22T09:18:05","slug":"hydrogen-capture-by-boron-a-crazy-reaction-path","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822","title":{"rendered":"Hydrogen capture by boron: a crazy reaction path!"},"content":{"rendered":"
\n

A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C).[1]<\/a><\/span> The mechanism involves an initial equilibrium between React<\/strong> and Int1<\/strong>, followed by capture of the hydrogen by Int1<\/strong> to form a 5-coordinate borane intermediate (Int2<\/strong> below, as per Figure 11).\u2021<\/sup> This was followed by assistance from a proximate basic nitrogen to complete the hydrogen capture via<\/em> a TS<\/strong> involving H-H cleavage. The forward free energy barrier to capture was ~11 kcal\/mol and ~4 kcal\/mol in the reverse direction (relative to the species labelled Int1<\/strong>), both suitably low for reversible hydrogen capture. Here I explore a simple variation to this fascinating reaction.\u221e<\/sup><\/p>\n


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

This variation involves transposing X and Y such that Y=N+<\/sup> and X=C–<\/sup> to form a carbon ylide such that X=C\u00a0becomes much more nucleophilic than the original nitrogen nucleophile. An animation of the full IRC\u2020<\/sup> (intrinsic reaction coordinate computed at \u03c9B97XD\/cc-pvtz; FAIR data doi: 10.14469\/hpc\/2704<\/a>)\u00a0is shown below.<\/p>\n

\"\"<\/p>\n

The profile shows that the reaction is concerted between the species labelled React<\/strong> and Prod<\/strong>; no sign of Int1<\/strong> and Int2!<\/strong><\/p>\n

    \n
  1. The region IRC -12 to -5 involves B-C bond cleavage. Because the C is so very nucleophilic, the 4-ring species labelled React<\/strong> becomes very stable and opening it requires a high barrier.<\/li>\n
  2. Between IRC -5 and 0, the BH2<\/sub> group rotates, losing its original interaction with the C to slowly create an empty acceptor orbital on the boron which can then interact with the incoming hydrogen.<\/li>\n
  3. At IRC= 0 (the transition state) the hydrogen has been captured by the boron to form a 5-coordinate species, in a manoeuvre that reminds one of the orbital capture of satellites by planets on their way to the outer reaches of the solar system. If the barrier to this capture is computed from IRC= -4 (the region of Int2<\/strong>) it is very much lower than the original system[1]<\/a><\/span>, again a reflection of the higher nucleophilicity of\u00a0X=C–<\/sup>.<\/li>\n
  4. The fly past continues until IRC= +7, at which point one end of the bound hydrogen has become suitably orientated to interact with the nucleophilic carbon via<\/em>\u00a0lone-pair donation into the acceptor H-H\u00a0\u03c3*<\/sup> orbital, thus helping to break it.<\/li>\n
  5. By IRC= +9, the H-H cleavage is complete.<\/li>\n
  6. By IRC= +13 the reaction has reached Prod<\/strong>, being overall ~ -12 kcal\/mol exothermic.<\/li>\n
  7. The overall thermochemistry is dominated by the potent carbon nucleophile in the reactant, which in turn makes this modification entirely useless for the purposes of a hydrogen-capture system!<\/li>\n<\/ol>\n

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

    The evolution of the dipole moment along the IRC shows very non-linear behaviour (such plots are rarely shown in most published IRC analyses; they should be!), ending of course with the ionic zwitterion that is the imminium borohydride Prod<\/strong>. Indeed the entire reaction coordinate is an unusually vivid example of a non-least motion path<\/em>!<\/p>\n

    \"\"<\/p>\n

    This simple atom transposition has given us a very instructive exercise in reaction paths, by-passing entirely both \u00a0Int1<\/strong> and Int2<\/strong> (making them hidden intermediates<\/em>), and converting React<\/strong>\u00a0\u2192 Prod<\/strong>\u00a0into a concerted reaction. It would be great to probe this convoluted journey using reaction dynamics!<\/p>\n

    \n

    \u221e<\/sup>Archived as DOI: 10.14469\/hpc\/3096<\/a><\/p>\n

    \u2021<\/sup> Such a species can be seen<\/a> as a hidden intermediate<\/i> in the mechanism of reduction of a carboxylic acid by diborane.<\/p>\n

    \u2020<\/sup>None were shown in the original study.[1]<\/a><\/span><\/p>\n

    References<\/h2>\n
    1. L. Li, M. Lei, Y. Xie, H.F. Schaefer, B. Chen, and R. Hoffmann, \"Stabilizing a different cyclooctatetraene stereoisomer\", Proceedings of the National Academy of Sciences<\/i>, vol. 114, pp. 9803-9808, 2017. https:\/\/doi.org\/10.1073\/pnas.1709586114<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C). The mechanism involves an initial equilibrium between React and Int1, followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate (Int2 below, as per Figure 11).\u2021 This was […]<\/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":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},"jetpack_post_was_ever_published":false},"categories":[1086],"tags":[2240,152,2239,1395,2242,2243,206,2241,1960,1431],"ppma_author":[2661],"class_list":["post-18822","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-ammonia-borane","tag-animation","tag-boranes","tag-chemistry","tag-cleaning-services","tag-company-react-group","tag-free-energy-barrier","tag-hydroboration","tag-hydrogen","tag-matter"],"yoast_head":"\nHydrogen capture by boron: a crazy reaction path! - 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=18822\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Hydrogen capture by boron: a crazy reaction path! - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C). The mechanism involves an initial equilibrium between React and Int1, followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate (Int2 below, as per Figure 11).\u2021 This was […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-09-21T06:55:06+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-09-22T09:18:05+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/09\/H-cap.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":"Hydrogen capture by boron: a crazy reaction path! - Henry Rzepa'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=18822","og_locale":"en_GB","og_type":"article","og_title":"Hydrogen capture by boron: a crazy reaction path! - Henry Rzepa's Blog","og_description":"A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C). The mechanism involves an initial equilibrium between React and Int1, followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate (Int2 below, as per Figure 11).\u2021 This was […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822","og_site_name":"Henry Rzepa's Blog","article_published_time":"2017-09-21T06:55:06+00:00","article_modified_time":"2017-09-22T09:18:05+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/09\/H-cap.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=18822#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Hydrogen capture by boron: a crazy reaction path!","datePublished":"2017-09-21T06:55:06+00:00","dateModified":"2017-09-22T09:18:05+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822"},"wordCount":564,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/09\/H-cap.svg","keywords":["Ammonia borane","animation","Boranes","Chemistry","Cleaning Services","Company: React Group","free energy barrier","Hydroboration","Hydrogen","Matter"],"articleSection":["reaction mechanism"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18822","name":"Hydrogen capture by boron: a crazy reaction path! 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A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I\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":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/acyloxy1-page001.svg","width":350,"height":200},"classes":[]},{"id":31140,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=31140","url_meta":{"origin":18822,"position":2},"title":"The fast disappearance of hydroxycarbene through hydrogen tunnelling – or is it really tunnelling?","author":"Henry Rzepa","date":"April 11, 2026","format":false,"excerpt":"In 2008, the previously elusive hydroxycarbene, H-C-OH was finally reported as having been captured by matrix isolation, accompanied by the observation that \"we unexpectedly find that H\u2013C\u2013OH rearranges to formaldehyde with a half-life of only 2h at 11K by pure hydrogen tunnelling through a large energy barrier in excess of\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":22541,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22541","url_meta":{"origin":18822,"position":3},"title":"The Willgerodt-Kindler Reaction: mechanistic reality check 1.","author":"Henry Rzepa","date":"July 21, 2020","format":false,"excerpt":"The Willgerodt reaction, discovered in 1887 and shown below, represents a transformation with a once famously obscure mechanism. 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This classic experiment conducted by Cotton (of quadruple bond fame) and Calderazzo in 1962 dates from an era when chemists conducted extensive kinetic analyses to back up any mechanistic speculations. Their suggested\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":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/11\/CO%2Bethene.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":11995,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11995","url_meta":{"origin":18822,"position":5},"title":"The wrong trousers: the anti-Markovnikov addition of borane to 2-methylpropene.","author":"Henry Rzepa","date":"March 2, 2014","format":false,"excerpt":"A staple of introductory undergraduate teaching in organic chemistry is Markovnikov's rule, which states: \"the addition of a protic acid HX to an alkene results in the acid hydrogen (H) becoming attached to the carbon with fewer alkyl substituents and the halide (X) group to the carbon with more alkyl\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/borane%2Bbutene.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\/18822","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=18822"}],"version-history":[{"count":16,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18822\/revisions"}],"predecessor-version":[{"id":18847,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18822\/revisions\/18847"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18822"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18822"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18822"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18822"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}