{"id":7027,"date":"2012-07-09T20:58:16","date_gmt":"2012-07-09T19:58:16","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=7027"},"modified":"2020-05-22T06:37:02","modified_gmt":"2020-05-22T05:37:02","slug":"joining-up-the-pieces-peroxidation-of-ethyne","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7027","title":{"rendered":"Joining up the pieces. Peroxidation of ethyne."},"content":{"rendered":"
\n

Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.<\/p>\n

    \n
  1. I had noted<\/a> that antiaromaticity in cyclopropenium anion is lessened by the system adopting gross geometric distortions, which take the anionic lone pair out of conjugation from the ring.<\/li>\n
  2. Similarly, cyclobutadiene can form a complex<\/a> with the guanidinium cation in which the anti-aromaticity is reduced by the formation of strong C…H-N hydrogen bonds.<\/li>\n
  3. Unhappy with modelling a cation without a counter-ion, I added one<\/a>. I noted that the cyclobutadiene+ ion pair was more stable in this more complete form.<\/li>\n
  4. My next connection is to a post on how ethyne reacts with peracetic acid<\/a>. The initial product of this reaction is oxirene, which like cyclobutadiene or cyclopropenium anion is anti-aromatic. This time, the liberated acetic acid forms a remarkably strong hydrogen bond to the oxygen of the antiaromatic ring as a way of reducing the antiaromaticity.\u00a0<\/li>\n
  5. Particularly noteworthy was that the initial attack of oxygen on the alkyne was very asymmetric. This reminded of another post<\/a> on the reaction of dichlorocarbene with ethene, which too is asymmetric, yet again to avoid an antiaromatic transition state. However, as the hydrogen bond\u00a0in 4<\/strong> above get stronger, the antiaromatic oxirene becomes symmetrical again. It is as if the hydrogen bond had replaced the need for asymmetry (as with 2 above).<\/li>\n
  6. Another asymmetric example<\/a> is the 2+2 closed shell cycloaddition of two ethenes, which adopt a different form of distortion.<\/li>\n<\/ol>\n

    The original alkyne+peracid study was conducted using a gas phase model. I decided to revisit it now, but to change the modelled medium from the gas phase to continuum water. I show the IRC (intrinsic reaction coordinates) for this reaction<\/a> in continuum water followed by the gas phase below (click on the animations to see the transition state model).<\/p>\n

    \"\"<\/p>\n

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

    \"\"<\/p>\n

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

    I want to compare the difference that introducing a model solvent (water) has made to the appearance of the reaction path.<\/p>\n

      \n
    1. In water, the symmetry of the forming antiaromatic oxirene ring is always maintained. There is no distortion; the combination of hydrogen bond, developing ionicity and its stabilization by the model solvent, appears to eliminate the need for such distortion. The free energy barrier, \u0394G\u2021<\/sup> (\u03c9B97XD\/6-311G(d,p) is 32.2 kcal\/mol, outside of a room temperature reaction.<\/li>\n
    2. In water, the proton transfer step comes much later, and is visible in the RMS gradient norm at +1.4.<\/li>\n
    3. In the gas phase, the IRC is much more complex (as previously noted). Pronounced asymmetry develops, and this only resymmetrises late on, when the hydrogen bond forms.<\/li>\n
    4. In the gas phase, the proton transfer occurs relatively early, and it cannot be found as a discrete feature in the RMS gradient norm plot.\u00a0<\/li>\n
    5. If a more acidic peracid is introduced, say\u00a0CF3<\/sub>CO3<\/sub>H, and the reaction is again simulated in water, the proton transfer is further delayed (below), and the barrier drops to\u00a0\u0394G\u2021<\/sup> 25.9 kcal\/mol, an entirely viable thermal reaction. I do not believe this particular variation has ever been tested experimentally;\u00a0anyone up for it?\u00a0\"\"<\/a><\/li>\n
    6. The product of the CF3<\/sub>CO3<\/sub>H reaction is shown below. It has a remarkably short predicted hydrogen bond of\u00a01.55\u00c5\u00a0between the oxirene and the trifluoracetic acid.\"\"<\/a><\/li>\n<\/ol>\n

      The take home message is that the very nature of a reaction, the geometry (symmetry) of the molecules taking part, and the timing of the changes can be very visibly changed by simulating the event with a solvent. In the past of course, all such computational studies were conducted purely as a gas phase model.<\/p>\n

      Postscript:<\/strong> The above shows how even a change in continuum solvent can affect the features of the reaction path. A rather greater perturbation is to change e.g.<\/em> the substituents on the alkyne. I have tried replacing one H with t-butyl, and the other with OH. The rationale for the former is that t-butyl acetylene is actually the substrate that this reaction has been performed on, and for OH that it pushes electrons into the oxirene, making it more anti-aromatic and hence more liable to avoid that antiaromaticity. Animation of the IRC for this combination<\/a> is shown below. Notice how the reaction now proceeds in a concerted manner directly from the alkyne to the hydroxy-carbene, without any sign of an intervening oxirene.\u00a0\"\"<\/a><\/p>\n

      The energy and gradient profiles for this variation are shown below. Notice in particular how the barrier has dropped; it is now a much easier reaction.\"\"<\/a><\/p>\n

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

      Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts. I had noted that antiaromaticity in cyclopropenium anion is lessened by the system adopting gross geometric distortions, which take […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[2327,1086],"tags":[855,145,22,854,843,858],"ppma_author":[2661],"class_list":["post-7027","post","type-post","status-publish","format-standard","hentry","category-curl-arrows","category-reaction-mechanism-2","tag-alkyne","tag-gas-phase","tag-gas-phase-model","tag-perepoxidation","tag-reaction-mechanism","tag-semantic-web-tools"],"yoast_head":"\nJoining up the pieces. Peroxidation of ethyne. - 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=7027\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Joining up the pieces. Peroxidation of ethyne. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts. I had noted that antiaromaticity in cyclopropenium anion is lessened by the system adopting gross geometric distortions, which take […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7027\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2012-07-09T19:58:16+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2020-05-22T05:37:02+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/07\/alkyne+pa_water.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":"Joining up the pieces. 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As a 2-electron thermal process, the second step proceeds with disrotation of the terminii. Can this stereochemistry be illustrated with a computed\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":"Pericylically assisted solvolysis. 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Most calculations indicate the force constant for an \"isolated\" symmetrical cation\u00a0is +ve, which means it is a true\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/b3lypd3bj.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":13394,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13394","url_meta":{"origin":7027,"position":2},"title":"How many water molecules does it take to ionise HCl?","author":"Henry Rzepa","date":"February 14, 2015","format":false,"excerpt":"According to Guggemos, Slavicek and Kresin, about 5-6!. This is one of those simple ideas, which is probably quite tough to do experimentally. It involved blasting water vapour through a pinhole, adding HCl and\u00a0measuring the dipole-moment induced deflection by an electric field. They\u00a0found\u00a0\"evidence for a noticeable rise in the dipole\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":6262,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6262","url_meta":{"origin":7027,"position":3},"title":"An exothermic E2 elimination: an unusual intrinsic reaction coordinate.","author":"Henry Rzepa","date":"February 6, 2012","format":false,"excerpt":"The previous post explored why E2 elimination reactions occur with an antiperiplanar geometry for the transition state. Here I have tweaked the initial reactant to make the overall reaction exothermic rather than endothermic as it was before. The change is startling. The exothermicity is of course due to the aromatisation\u2026","rel":"","context":"In \"conformational analysis\"","block_context":{"text":"conformational analysis","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=conformational-analysis"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/02\/E2-benzo.svg","width":350,"height":200},"classes":[]},{"id":3003,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3003","url_meta":{"origin":7027,"position":4},"title":"Janus mechanisms (the past and the future): Reactions of the diazonium cation.","author":"Henry Rzepa","date":"December 11, 2010","format":false,"excerpt":"Janus was the mythological Roman god depicted as having two heads facing opposite directions, looking simultaneously into the past and the future. Some of the most ancient (i.e. 19th century) known reactions can be considered part of a chemical mythology; perhaps it is time for\u00a0a Janus-like look into their future.\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\/12\/diazonium.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23522,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23522","url_meta":{"origin":7027,"position":5},"title":"A computational mechanism for the aqueous hydrolysis of a ketal to a ketone and alcohol.","author":"Henry Rzepa","date":"April 1, 2021","format":false,"excerpt":"The previous post was about an insecticide and made a point that the persistence of both insecticides and herbicides is an important aspect of their environmental properties. Water hydrolysis will degrade them, a typical residency time being in the order of a few days. I noted in passing a dioxepin-based\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/03\/R-1024x699.jpg?resize=350%2C200&ssl=1","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","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\/7027","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=7027"}],"version-history":[{"count":38,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7027\/revisions"}],"predecessor-version":[{"id":22377,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7027\/revisions\/22377"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=7027"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=7027"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=7027"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=7027"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}