{"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_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":[],"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. 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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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