{"id":8961,"date":"2013-01-06T17:35:28","date_gmt":"2013-01-06T17:35:28","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=8961"},"modified":"2013-09-05T06:36:23","modified_gmt":"2013-09-05T05:36:23","slug":"the-mechanism-of-the-benzidine-rearrangement","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8961","title":{"rendered":"The mechanism of the Benzidine rearrangement."},"content":{"rendered":"
\n

The benzidine rearrangement is claimed to be an example of the quite rare\u00a0[5,5] sigmatropic migration[1]<\/a><\/span>, which is a ten-electron homologation<\/a> of the very common [3,3] sigmatropic reaction (e.g.<\/em> the Cope or Claisen). Some benzidine rearrangements are indeed thought to go through the [3,3] route[2]<\/a><\/span>. The topic has been reviewed here[3]<\/a><\/span>.<\/p>\n

\"benzidine\"<\/p>\n

In this post, I offer a calculated transition state<\/a> and IRC<\/a> for this reaction, to see what insights might accrue. How was this obtained?<\/p>\n

    \n
  1. At the \u03c9B97XD\/6-311G(d,p)\/SCRF=water level. This procedure would allow for any dispersion-like effects to be allowed for in the \u03c0-\u03c0-stacking.\u00a0<\/li>\n
  2. The rearrangement is normally promoted by acid, and the active species is thought to be diprotonated[4]<\/a><\/span>\u2021<\/sup> (although monoprotonated catalysis<\/a> is also observed[1]<\/a><\/span>. Here I report just the diprotonated route, together with chloride anions to balance the charges, and have added a continuum water field to allow this double ion-pair to be at least partially stabilised.<\/li>\n
  3. The rate determining step is the N-N cleavage\/C-C bond formation. This is followed by presumed rapid proton transfers, which are not modelled here.<\/li>\n<\/ol>\n\n\n\n\n
    \n
    \"The

    The [5,5] transition state for the benzidine rearrangement. Click for 3D.<\/p><\/div>\n<\/td>\n

    		\"benzidine-55\"<\/td>\n<\/tr>\n
    \"benzidine-55E\"<\/td>\n\"benzidine-55G\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    This [5,5] transition state is 2.9 kcal\/mol lower in \u0394G\u2021<\/sup>298<\/sub> than the transition state<\/a> for the isomeric [3,3] rearrangement. The NCI (non-covalent-interactions) shows the forming C-C bond to be on the border of covalent, and non-covalent (blue), but that the\u00a0\u03c0-\u03c0-stacking region is all weakly attractive (green). You can also observe the strong hydrogen bonds between the chloride anion and an N-H group (blue), and the weak attractive zones between the two nitrogen centres, between the chloride and the ortho-C-H hydrogens, and even between the two chloride anions (blue-green or green). I should point out that the initial position for these anions was over the aryl ring, but they migrated to the NH region during optimisation of the transition state.<\/p>\n

    \"NCI

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

    The molecular electrostatic potential (isosurface = 0.11 au) shows both aryl rings as a single unit attracted by a positive potential (blue)<\/p>\n

    \"Calculated

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

    The highest-occupied molecular orbital shows the two bonds involved in the [5,5] shift (N-N and C-C) are both bonding, but more significantly, the central region of the two stacked aryl rings is also bonding. This is a clear manifestation of a \u03c0-complex, which the benzidine rearrangement has often (and it has to be said controversially) described as, and which elevates this particular reaction from that of a simple bond forming\/bond cleaving sigmatropic. Another way of looking at it is that secondary orbital interactions (such as often invoked in Diels-Alder cycloadditions) are exceptionally important here.<\/p>\n

    \"HOMO

    HOMO for 5,5 benzidine rearrangement. Click for 3D.<\/p><\/div>\n

    The LUMO is strongly antibonding in that region; indeed adding two electrons to form a 12-electron process would be strongly destabilising. In this regard, this unusual sigmatropic reaction follows the same 4n+2 electron rule as more conventional ones.<\/p>\n

    \"LUMO.

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

    The next two diagrams illustrate the competing (higher energy) [3,3] shift, which also has some \u03c0-complex character.<\/p>\n

    \"A

    A [3,3] alternative to the benzidine rearrangement. Click for 3D.<\/p><\/div>\n

     <\/p>\n

    \"NCI

    NCI surface for 3,3 rearrangement. Click for 3D.<\/p><\/div>\n

    I will end with three autobiographical notes.<\/p>\n

      \n
    1. The benzidine rearrangement was one of the earliest reactions I did in my home laboratory, at the age of about \u00a013. As I recollect, I prepared about 1.5 grams (blissfully ignorant of how carcinogenic it is), and used it via<\/em> diazotization to couple to phenol. My fascination with chemistry most certainly started with colour (and how to express the bonding in nitric oxide).<\/li>\n
    2. About eight years later, I was about to commence my Ph.D. studies. The objective was to use kinetic isotope effects to infer the structure of transition states. In my case (proton transfers to indoles) I never did achieve this objective. But it is noteworthy that the mechanism of the benzidine rearrangement was largely unravelled using such isotopic studies.<\/li>\n
    3. By 1974 as a post-doctoral researcher, I had moved on to studying mechanisms using \u00a0quantum theory and had decided that it was easier to invert the use of isotope effects by predicting a transition structure using this method, and then seeing if the computed isotope effects matched the experiment. We did this for the Diels-Alder reaction[5]<\/a><\/span> and more generally[6]<\/a><\/span>, and then for some gas-phase eliminations[7]<\/a><\/span>, this latter being my first entirely independent publication.<\/li>\n
    4. So, putting all this together, one might infer that armed with a computed transition state structure for the benzidine rearrangement, it is trivial to compute the kinetic isotope effects and hence to see if they correspond to those measured. You might expect a report on this in a future post here<\/a>.<\/li>\n<\/ol>\n
      \n

      \u2021<\/sup> Crystal structures of diprotonated dimethyl hydrazines[4]<\/a><\/span> show a N-N bond length of ~1.45\u00c5 (typical counter-anions being nitrate, perchlorate or sulfate). That calculated for the diprotonated diphenyl hydrazine is ~2.5\u00c5, which suggests that with the phenyl group, electrons from the N-N region may be borrowed to contribute to the\u00a0\u03c0-\u03c0-complex.<\/p>\n

      References<\/h2>\n
      1. H.J. Shine, K.H. Park, M.L. Brownawell, and J. San Filippo, \"Benzidine rearrangements. 19. The concerted nature of the one-proton rearrangement of 2,2'-dimethoxyhydrazobenzene\", Journal of the American Chemical Society<\/i>, vol. 106, pp. 7077-7082, 1984. https:\/\/doi.org\/10.1021\/ja00335a035<\/a>\n\n<\/li>\n
      2. H.J. Shine, L. Kupczyk-Subotkowska, and W. Subotkowski, \"Heavy-atom kinetic isotope effects in the acid-catalyzed rearrangement of N-2-naphthyl-N'-phenylhydrazine. Rearrangement is shown to be a concerted process\", Journal of the American Chemical Society<\/i>, vol. 107, pp. 6674-6678, 1985. https:\/\/doi.org\/10.1021\/ja00309a041<\/a>\n\n<\/li>\n
      3. H.J. Shine, \"Reflections on the \u03c0\u2010complex theory of benzidine rearrangements\", Journal of Physical Organic Chemistry<\/i>, vol. 2, pp. 491-506, 1989. https:\/\/doi.org\/10.1002\/poc.610020702<\/a>\n\n<\/li>\n
      4. C.M. Sabat\u00e9, and H. Delalu, \"Energetic Salts of Symmetrical Dimethylhydrazine (SDMH)\", European Journal of Inorganic Chemistry<\/i>, vol. 2012, pp. 866-877, 2011. https:\/\/doi.org\/10.1002\/ejic.201101115<\/a>\n\n<\/li>\n
      5. M.J.S. Dewar, S. Olivella, and H.S. Rzepa, \"Ground states of molecules. 49. MINDO\/3 study of the retro-Diels-Alder reaction of cyclohexene\", Journal of the American Chemical Society<\/i>, vol. 100, pp. 5650-5659, 1978. https:\/\/doi.org\/10.1021\/ja00486a013<\/a>\n\n<\/li>\n
      6. S.B. Brown, M.J.S. Dewar, G.P. Ford, D.J. Nelson, and H.S. Rzepa, \"Ground states of molecules. 51. MNDO (modified neglect of diatomic overlap) calculations of kinetic isotope effects\", Journal of the American Chemical Society<\/i>, vol. 100, pp. 7832-7836, 1978. https:\/\/doi.org\/10.1021\/ja00493a008<\/a>\n\n<\/li>\n
      7. H.S. Rzepa, \"MNDO SCF-MO calculations of kinetic isotope effects for dehydrochlorination reactions of chloroalkanes\", Journal of the Chemical Society, Chemical Communications<\/i>, pp. 939, 1981. https:\/\/doi.org\/10.1039\/c39810000939<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

        The benzidine rearrangement is claimed to be an example of the quite rare\u00a0[5,5] sigmatropic migration, which is a ten-electron homologation of the very common [3,3] sigmatropic reaction (e.g. the Cope or Claisen). Some benzidine rearrangements are indeed thought to go through the [3,3] route. The topic has been reviewed here. In this post, I offer […]<\/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":[4],"tags":[68,2651,979,2650,843],"ppma_author":[2661],"class_list":["post-8961","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-higher-energy","tag-historical","tag--complex","tag-pericyclic","tag-reaction-mechanism"],"yoast_head":"\nThe mechanism of the Benzidine rearrangement. - 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=8961\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The mechanism of the Benzidine rearrangement. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The benzidine rearrangement is claimed to be an example of the quite rare\u00a0[5,5] sigmatropic migration, which is a ten-electron homologation of the very common [3,3] sigmatropic reaction (e.g. the Cope or Claisen). 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In this post, I offer […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8961\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-01-06T17:35:28+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-09-05T05:36:23+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/benzidine.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=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"The mechanism of the Benzidine rearrangement. - 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=8961","og_locale":"en_GB","og_type":"article","og_title":"The mechanism of the Benzidine rearrangement. - Henry Rzepa's Blog","og_description":"The benzidine rearrangement is claimed to be an example of the quite rare\u00a0[5,5] sigmatropic migration, which is a ten-electron homologation of the very common [3,3] sigmatropic reaction (e.g. the Cope or Claisen). 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Computed kinetic isotope effects.","author":"Henry Rzepa","date":"January 11, 2013","format":false,"excerpt":"Kinetic isotope effects have become something of a lost art when it comes to exploring reaction mechanisms. But in their heyday they were absolutely critical for establishing the mechanism of the benzidine rearrangement. This classic mechanism proceeds via bisprotonation of diphenyl hydrazine, but what happens next was the crux. Does\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":9018,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9018","url_meta":{"origin":8961,"position":1},"title":"Hidden intermediates in the benzidine rearrangement. The monoprotonated mechanism.","author":"Henry Rzepa","date":"January 8, 2013","format":false,"excerpt":"Eagle-eyed footnote readers might have spotted one at the bottom of the post on the benzidine rearrangement. I was comparing the N-N bond lengths in crystal structures of known diprotonated hydrazines (~1.45\u00c5) with the computed N-N bond length at the start point of the intrinsic reaction coordinate for the [5,5]\u2026","rel":"","context":"In \"free energy barrier\"","block_context":{"text":"free energy barrier","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=free-energy-barrier"},"img":{"alt_text":"Transition state between p-complex and N-N diprotonated diphenyhydrazine. Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/pi-TS.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":10743,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10743","url_meta":{"origin":8961,"position":2},"title":"Mechanism of the Boekelheide rearrangement","author":"Henry Rzepa","date":"June 26, 2013","format":false,"excerpt":"A reader asked me about the mechanism of\u00a0the reaction of 2-picoline N-oxide with acetic anhydride to give 2-acetoxymethylpyridine (the\u00a0Boekelheide Rearrangement). He wrote \"\u00a0I don't understand why the system should prefer to go via fragmentation-recombination (... the evidence being that\u00a0oxygen labelling shows scrambling)\u00a0when there is an easy concerted pathway available (...\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":"Boek1","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/06\/Boek1.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":9135,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9135","url_meta":{"origin":8961,"position":3},"title":"Why is N,O-diphenyl hydroxylamine (PhNHOPh) unknown?","author":"Henry Rzepa","date":"January 16, 2013","format":false,"excerpt":"If you search e.g. Scifinder for N,O-diphenyl hydroxylamine (RN\u00a024928-98-1) there is just one literature citation, to a 1962 patent. Nothing else; not even a calculation (an increasing proportion of the molecules reported in Chemical Abstracts have now only ever been subjected to calculation, not synthesis).\u00a0A search of Reaxys also offers\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":9186,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9186","url_meta":{"origin":8961,"position":4},"title":"The \u03c0-complex in the benzidine rearrangement: a molecular orbital analysis.","author":"Henry Rzepa","date":"January 18, 2013","format":false,"excerpt":"Michael Dewar famously implicated a so-called\u00a0\u03c0-complex in the benzidine rearrangement, back in the days when quantum mechanical calculations could not yet provide a quantitatively accurate reality check. 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":7678,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7678","url_meta":{"origin":8961,"position":5},"title":"Frozen Semibullvalene: a holy grail (and a bis-homoaromatic molecule).","author":"Henry Rzepa","date":"September 15, 2012","format":false,"excerpt":"Semibullvalene is an unsettling molecule. Whilst it has a classical structure describable by a combination of Lewis-style two electron and four electron bonds, its NMR behaviour reveals it to be highly fluxional. This means that even at low temperatures, the position of these two-electron bonds rapidly shifts in the equilibrium\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\/09\/CAZFUE1.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\/8961","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=8961"}],"version-history":[{"count":43,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/8961\/revisions"}],"predecessor-version":[{"id":11155,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/8961\/revisions\/11155"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=8961"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=8961"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=8961"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=8961"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}