{"id":4751,"date":"2011-09-01T12:58:46","date_gmt":"2011-09-01T12:58:46","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=4751"},"modified":"2011-11-28T13:15:21","modified_gmt":"2011-11-28T13:15:21","slug":"computational-reality-checks-for-mechanistic-speculations","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4751","title":{"rendered":"Computational “reality checks” for mechanistic speculations."},"content":{"rendered":"
\n

I have mentioned<\/a> Lewis a number of times in these posts; his suggestion of the shared electron covalent bond still underpins much chemical thinking. Take for example mechanistic speculations on the course of a reaction, a very common indulgence in almost all articles reporting such, and largely based on informed\u00a0\u00a0arrow pushing<\/a><\/em>. This process is bound to follow the rules of reasonable Lewis structures for any putative intermediates. Here, I suggest that we are now firmly in an era where such speculations must of necessity be backed up by quantum mechanical estimates of the energies and structures. I would propose that journals routinely encourage referees to insist on such (additional) checks. Let me give one specific example of the need to do this (part of a follow up to an earlier article I blogged on<\/a> previously).<\/p>\n

\"\"<\/a>

Scheme 1 (reproduced from 10.1002\/chem.201100693 )<\/p><\/div>\n

The example is found as\u00a0scheme 1<\/strong> of an\u00a0article written by Legrand, Gilles, Petit, van\u2005der\u2005Lee and Barboiu entitled “Unprecedented Synthesis of 1,3-Dimethylcyclobutadiene in the Solid State and Aqueous Solution<\/em>” (DOI:\u00a010.1002\/chem.201100693<\/a>; \u00a0Scheme 1 reproduced here \u00a0with the permission of the publishers). Structures\u00a01<\/strong>\u00a0– 3<\/strong>\u00a0are my additions, and are not present in scheme 1<\/strong> of the above article.<\/p>\n

\"\"<\/a>

Possible species involved in the mechanism for photochemical irradiation of dimethyl pyrone.<\/p><\/div>\n

The scientific problem is to identify what the products are of photolysis of\u00a0Me2<\/sub>1<\/strong>. The species is contained as a guest inside a calixarene host, the whole assembly being dissolved in water (D2<\/sub>O). This was photolysed and the products characterised by (inter alia<\/em>) their\u00a01<\/sup>H NMR spectra, Figure 7<\/a>. Focus in\u00a0particular on\u00a07b<\/strong>, which shows a set of five spectra that are claimed to identify the consecutive species\u00a0Me2<\/sub>1<\/strong>, Me2<\/sub>2<\/strong>, (Me2<\/sub>3<\/strong>\u00a0or 1<\/strong>),\u00a0Me2<\/sub>CBDS<\/sup>\/CO2<\/sub><\/strong>, Me2<\/sub>CBDR<\/sup><\/strong> and Me2<\/sub>4<\/strong>\u00a0as the outcomes of photolysis at “different irradiation times at l=320\u2013500 nm or at l=190\u2013500 nm<\/em>“.<\/p>\n

\"\"<\/a>

Figure 7 (taken from 10.1002\/chem.201100693, reproduced with permission of publisher )<\/p><\/div>\n

How might one apply a computational reality check to this scheme? Lewis himself might have ventured to suggest that representation\u00a0Me2<\/sub>3 <\/strong>does not adhere to his rules; a modern chemistry student would draw it instead as 2<\/strong>, a vinyl zwitterion. This species in turn could either eliminate carbon monoxide (red arrow) or ring close to give the unusual ylid 3 <\/strong>(blue arrow).\u00a0In fact DFT calculations on the isolated molecules in water (\u03c9B97XD\/6-311G(d,p)\/SCRF=water<\/a>) indicate that the C-O bond in an isolated molecule of\u00a0Me2<\/sub>3\u00a0<\/strong>does not persist and fragments to carbon monoxide and an alkoxy zwitterion,\u00a0making it around ~36.5 kcal\/mol higher in free energy than the alternative zwitterion<\/a> 1<\/strong>. The third species 3<\/strong>\u00a0is somewhat more stable, being ~20 kcal\/mol above 1<\/strong>. Calculations also reveal that whilst rectangular Me2<\/sub>CBDR<\/sup><\/strong> is obtained on the singlet surface, the square Me2<\/sub>CBDS<\/sup>\/CO2<\/sub><\/strong> can only be obtained on the triplet surface. This state however is\u00a0~8-10 kcal\/mol higher in energy and unlikely to have a long lifetime before it decays down to the singlet surface. One could study all the species in the scheme above in this manner, but that analysis is for another place and time.<\/p>\n

Until relatively recently, such reality checks would be all one might attempt computationally. But these experiments were NOT conducted on isolated molecules in solution, they were done in the presence of a calixarene host. Could that change things? Zwitterion 1<\/strong> can be placed inside this cavity<\/a>\u00a0and the calculation repeated (again simulating solvent water), as can 2<\/strong>. In fact the latter spontaneously collapses to 3<\/strong>, and now has an energy ~ 27 kcal\/mol higher than 1<\/strong>. Whether 1<\/strong> itself (or indeed Me2<\/sub>CBDR<\/sup><\/strong>)\u00a0has any persistent lifetime is another issue, and one not addressed in this blog post.<\/p>\n

In fact, the reality check has another purpose, which is to stimulate other ideas. In this case for example one could regard 3<\/strong> as a carbene, in which case one might ask if coordination of the carbene to a suitable metal might be a stabilizing mode. Amazingly, a number of such systems are known! I show just one below.<\/p>\n\n\n\n
\n

\"\"
\nSCHXFe. Click for 3D structure.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

<\/strong>There is a lot more that could be said (and written) about this article<\/a>, including discussion of the\u00a01<\/sup>H NMR spectra, but I will stop at this point. Hopefully, I have shown how simple computational reality checks on a proposed mechanism can easily result in both unexpected outcomes and ideas for new chemistry!<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

I have mentioned Lewis a number of times in these posts; his suggestion of the shared electron covalent bond still underpins much chemical thinking. Take for example mechanistic speculations on the course of a reaction, a very common indulgence in almost all articles reporting such, and largely based on informed\u00a0\u00a0arrow pushing. This process is bound […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[288,658,396,659,24,40,655,2650,656,653,654,657],"ppma_author":[2661],"class_list":["post-4751","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-3-dimethylcyclobutadiene","tag-blog-server","tag-calixarene","tag-chemical-thinking","tag-energy","tag-free-energy","tag-lewis","tag-pericyclic","tag-petit","tag-photolysis","tag-square-me","tag-suitable-metal"],"yoast_head":"\nComputational "reality checks" for mechanistic speculations. - 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=4751\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Computational "reality checks" for mechanistic speculations. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I have mentioned Lewis a number of times in these posts; his suggestion of the shared electron covalent bond still underpins much chemical thinking. 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This process is bound […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4751\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-09-01T12:58:46+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-11-28T13:15:21+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/nsch001.gif\" \/>\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":"Computational \"reality checks\" for mechanistic speculations. - 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=4751","og_locale":"en_GB","og_type":"article","og_title":"Computational \"reality checks\" for mechanistic speculations. - Henry Rzepa's Blog","og_description":"I have mentioned Lewis a number of times in these posts; his suggestion of the shared electron covalent bond still underpins much chemical thinking. 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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. 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Here is a quantum energetic exploration of what might happen when a second LAH is added\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":"","src":"","width":0,"height":0},"classes":[]},{"id":14984,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14984","url_meta":{"origin":4751,"position":4},"title":"The atom and the molecule: A one-day symposium on 23 March, 2016 celebrating Gilbert N. Lewis.","author":"Henry Rzepa","date":"December 11, 2015","format":false,"excerpt":"You might have noticed the occasional reference here to the upcoming centenary of the publication of Gilbert N. Lewis' famous article entitled \"The atom and the molecule\". A symposium exploring his\u00a0scientific impact and legacy\u00a0will be held in London on March 23, 2016, exactly 70 years to the day since his\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":2559,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2559","url_meta":{"origin":4751,"position":5},"title":"(Almost) 100 years of Lewis structures: are they still fit for purpose?","author":"Henry Rzepa","date":"September 27, 2010","format":false,"excerpt":"The molecule below was characterised in 1996 (DOI: 10.1246\/cl.1996.489) and given the name tris(dithiolene)vanadium (IV). No attempt was made in the original article to give this molecule a Lewis structure using Lewis electron pair bonds. This blog will explore some of the issues that arise when this is attempted.1 The\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.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/V1.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\/4751","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=4751"}],"version-history":[{"count":1,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4751\/revisions"}],"predecessor-version":[{"id":5679,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4751\/revisions\/5679"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4751"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4751"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4751"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=4751"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}