{"id":9018,"date":"2013-01-08T12:58:47","date_gmt":"2013-01-08T12:58:47","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=9018"},"modified":"2013-01-08T15:14:49","modified_gmt":"2013-01-08T15:14:49","slug":"hidden-intermediates-in-the-benzidine-rearrangement-the-monoprotonated-mechanism","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9018","title":{"rendered":"Hidden intermediates in the benzidine rearrangement. The monoprotonated mechanism."},"content":{"rendered":"
\n

Eagle-eyed footnote readers might have spotted one at the bottom of the post on the benzidine rearrangement<\/a>. 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] sigmatropic rearrangement of di-N-protonated diphenylhydrazine\u00a0(the active species in the benzidine rearrangement itself), which was some 1\u00c5 longer. This post explores the implications of this oddity.<\/p>\n

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

My start point however is actually the mono-N-protonated system. The IRC<\/a> for the calculated transition state<\/a> is shown below. The activation barrier is a lot higher than with the diprotonated route, but I want to bring to your attention a feature at IRC = +5 to +3. At this point the RMS gradient norm dips, approaching but not quite reaching zero. This is what is called a hidden intermediate<\/em>, an intermediate that does not quite form.\u2021<\/sup> It is in this region that the N-N bond length changes from the value of about 1.45\u00c5 for the monoprotonated hydrazine, to around 2.5\u00c5 at the point of the “hidden intermediate”. This represents the formation of the\u00a0\u03c0-\u03c0-stacked complex as the preamble to the actual rearrangement, the transition state for which is of course reached at IRC =0.0.\u00a0For this system, the [5,5] sigmatropic is actually slightly higher ( \u0394G\u2021<\/sup>298<\/sub>\u00a0+2.4 kcal\/mol) than the competing [3,3] rearrangement<\/a>, which also shows that hidden intermediate<\/em> ( at IRC<\/a> ~+2.0). This close balance between the [3,3] and the [5,5] mechanisms suggests that factors such as ring substituents, counter-ion, solvent etc may in fact be able to swing this balance one way or the other.\u00a0<\/p>\n\n\n\n\n
\u00a0
\n
\"The

The 5,5, sigmatropic rearrangement of monoprotonated diphenylhydrazine. Click for 3D<\/p><\/div>\n<\/td>\n<\/tr>\n

\u00a0\"benzidine-HCl-55E\"<\/td>\n\"benzidine-HCl-55G\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n\n\n
\n
\"The

The 3,3 sigmatropic rearrangement of monoprotonated diphenylhydrazine. Click for 3D.<\/p><\/div>\n<\/td>\n<\/tr>\n

\"benzidine-HCl-33E\"<\/td>\n\"benzidine-HCl-33G\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Which brings us back to the diprotonated species, the one with the N-N bond length of 2.53\u00c5. This is a stable minimum<\/a> (i.e.<\/em> the RMS gradient norm is<\/strong><\/em> zero) with no imaginary frequencies computed, and hence it is no longer a hidden intermediate<\/em>, but an exposed \u03c0-complex<\/strong><\/em>. Adding that second proton has stabilised it considerably. It is higher in\u00a0\u0394G298<\/sub> than the anti-conformation<\/a>\u00a0of diprotonated diphenylhydrazine by 6.1 kcal\/mol, the latter having the normal N-N bond length of 1.46\u00c5. The free energy barrier from the \u03c0-complex to the transition state for [5,5] rearrangement (shown in previous post) is a mere 2.4 kcal\/mol. The barrier from the same \u03c0-complex to the transition state (N-N length 1.97\u00c5<\/a>) leading back to N-N diprotonated diphenylhydrazine is also small, 3.1 kcal\/mol, so this \u03c0-complex<\/strong><\/em>\u00a0is bounded only by small barriers and hence is very unlikely to be directly detected.<\/p>\n\n\n\n\n
\n
\"The

The benzidine \u03c0-complex. Click for 3D.<\/p><\/div>\n<\/td>\n

\n
\"Anti-diprotonated

Anti-diprotonated diphenyl hydrazine. Click for 3D.<\/p><\/div>\n<\/td>\n<\/tr>\n

\n
\"Transition

Transition state between \u03c0-complex and N-N diprotonated diphenyhydrazine. Click for 3D.<\/p><\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

To conclude, mono-protonated diphenyl hydrazine\u2020<\/sup> rearranges to the 4,4′-diaminobiphenyl via<\/em> the so-called benzidine rearrangement by a concerted process that involves a hidden \u03c0-complex<\/strong> forming before the transition state is reached. Diprotonation exposes this hidden complex formed from diphenylhydrazine. This complex is the true starting point for the [5,5] sigmatropic rearrangement (if it can still be called that). The overall reaction becomes more exothermic by in effect separating the two positive charges resulting from nitrogen diprotonation onto the two phenyl rings, an affect which also encourages the \u03c0-complex<\/strong>\u00a0to form.<\/p>\n

\n

\u2021<\/sup>Another good example of such a species is the intermediate carbocation in the solvolysis of t-butyl chloride<\/a>. This too is hidden.<\/p>\n

\u2020<\/sup>It is rather curious that\u00a0Ph-NH-O-Ph is in effect unknown (apart from one patent).\u00a0Could it be that it cannot be prevented from rearranging by the same mechanism as Ph-NH-NH-Ph?<\/p>\n

\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

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] sigmatropic rearrangement of di-N-protonated diphenylhydrazine\u00a0(the […]<\/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_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":[],"tags":[206,843],"ppma_author":[2661],"class_list":["post-9018","post","type-post","status-publish","format-standard","hentry","tag-free-energy-barrier","tag-reaction-mechanism"],"yoast_head":"\nHidden intermediates in the benzidine rearrangement. The monoprotonated mechanism. - 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=9018\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Hidden intermediates in the benzidine rearrangement. The monoprotonated mechanism. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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] sigmatropic rearrangement of di-N-protonated diphenylhydrazine\u00a0(the […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9018\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-01-08T12:58:47+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-01-08T15:14:49+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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Hidden intermediates in the benzidine rearrangement. The monoprotonated mechanism. - 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=9018","og_locale":"en_GB","og_type":"article","og_title":"Hidden intermediates in the benzidine rearrangement. The monoprotonated mechanism. - Henry Rzepa's Blog","og_description":"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] sigmatropic rearrangement of di-N-protonated diphenylhydrazine\u00a0(the […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9018","og_site_name":"Henry Rzepa's Blog","article_published_time":"2013-01-08T12:58:47+00:00","article_modified_time":"2013-01-08T15:14:49+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/benzidine.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=9018#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9018"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Hidden intermediates in the benzidine rearrangement. 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Some benzidine rearrangements are indeed thought to go through the [3,3] route. The topic has been reviewed here.\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":"NCI surface. Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/benzidinenci.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":9186,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9186","url_meta":{"origin":9018,"position":1},"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":9135,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9135","url_meta":{"origin":9018,"position":2},"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":9105,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9105","url_meta":{"origin":9018,"position":3},"title":"The Benzidine rearrangement. 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":9218,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9218","url_meta":{"origin":9018,"position":4},"title":"Aromaticity in the benzidine-like \u03c0-complex formed from PhNHOPh.","author":"Henry Rzepa","date":"January 19, 2013","format":false,"excerpt":"The transient \u03c0-complex formed during the \"[5,5]\" sigmatropic rearrangement of protonated N,O-diphenyl hydroxylamine can be (formally) represented as below, namely the interaction of a six-\u03c0-electron aromatic ring (the phenoxide anion 2) with a\u00a0four-\u03c0-electron phenyl dication-anion pair 1. Can one analyse this interaction in terms of aromaticity? I showed previously that\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":"pi-QTAIM","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/pi-QTAIM.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":10252,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10252","url_meta":{"origin":9018,"position":5},"title":"Why diphenyl peroxide does not exist.","author":"Henry Rzepa","date":"April 29, 2013","format":false,"excerpt":"A few posts back, I explored the \"benzidine rearrangement\" of diphenyl hydrazine. This reaction requires diprotonation to proceed readily, but we then discovered that replacing one NH by an O as in N,O-diphenyl hydroxylamine required only monoprotonation to undergo an equivalent facile rearrangement. So replacing both NHs by O to\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":[]}],"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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9018","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=9018"}],"version-history":[{"count":38,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9018\/revisions"}],"predecessor-version":[{"id":9084,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9018\/revisions\/9084"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9018"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9018"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9018"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=9018"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}