{"id":14575,"date":"2015-09-24T14:10:05","date_gmt":"2015-09-24T13:10:05","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14575"},"modified":"2015-09-25T16:01:46","modified_gmt":"2015-09-25T15:01:46","slug":"isoelectronic-games-the-co-analogue-of-diazirenes-as-an-intriguing-species","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575","title":{"rendered":"Isoelectronic games: the CO analogue of diazirines as an intriguing species?"},"content":{"rendered":"
\n

How does an anaesthetic work? Surprisingly, it is only recently[1]<\/a><\/span> that the possible binding sites of the anaesthetic propofol (2,6-di-isopropylphenol) have been identified using a technique known as photoaffinity labelling.[2]<\/a><\/span> A propofol analogue was constructed[1]<\/a><\/span> by replacing one of\u00a0the isopropyl groups with a trifluoromethyl diazirine group (R=CF3<\/sub>, X=Y=N below). Upon photolysis, this species looses nitrogen and forms a carbene as a reactive species, which with further chemistry binds covalently[2]<\/a><\/span> to adjacent amino acids in the binding pocket.These modified segments could then be analysed by mass spectrometry.[1]<\/a><\/span> An isomer of\u00a0\u00a0diazirine is\u00a0diazomethane<\/a>, which is some 11 kcal\/mol lower in free energy, but fortunately the diazirene is preventing from thermally isomerising to this species by a large kinetic barrier. That was the intro; now for a connection<\/strong>.\u2021<\/sup> I recently attended a presentation on another medical topic, the therapeutic uses of carbon monoxide.[3]<\/a><\/span> In higher concentrations it is notoriously lethal, but with appropriate delivery\u00a0it can be\u00a0therapeutic. So,\u00a0intertwingling, I asked myself what the properties of the carbon monoxide isoelectronic analogue of a diazirine might be (X=C, Y=O below).\u00a0<\/p>\n

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

Firstly, a search using Scifinder. More than 102 million molecules and substances are reported there. Of course, that does not mean the molecule actually exists, since many structures are only known by calculation! But I could not find the CO analogue using a sub-structure search. So this simple isoelectronic analogue of a very well-known molecule type is not apparently well-known then (although I feel sure that a theoretical chemist must have calculated it at some stage,\u2020<\/sup> even if the results were not reported and abstracted by CAS). Here is\u00a0a \u03c9B97XD\/6-311G(d,p)\/SCRF=nitromethane set of calculations (kcal\/mol).<\/p>\n\n\n\n\n\n
Species<\/th>\n\u0394\u0394G298<\/sub> ring<\/th>\n\u0394\u0394G298<\/sub> linear<\/th>\n\u0394G\u2020<\/sup> XY extrusion<\/th>\n\u0394G\u2020<\/sup> ring opening<\/th>\n<\/tr>\n
X=Y=N<\/td>\n0.0[4]<\/a><\/span> \u00a0<\/td>\n-11.0[5]<\/a><\/span><\/td>\n36.1[6]<\/a><\/span><\/td>\n—<\/td>\n<\/tr>\n
X=C, Y=O<\/td>\n0.0[7]<\/a><\/span><\/td>\n-63.3[8]<\/a><\/span><\/td>\n27.3[9]<\/a><\/span><\/td>\n46.8[10]<\/a><\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

We learn the following:<\/p>\n

    \n
  1. The CO analogue is far less stable as a ring than the NN equivalent, but it is a clear-cut minimum in the energy surface.<\/li>\n
  2. In the absence of any other conditions (for example protons), the free energy barrier for extruding CO is actually quite high, being only a little lower than the diazirine itself. The latter is thermally reasonably stable and not a fragile molecule at all. At face value therefore if made, such a cyclo-oxenium ylid might\u00a0have a long enough “shelf life” to be detectable or trappable, certainly at lower temperatures.\u00a0<\/li>\n
  3. It shows an even higher barrier to ring opening to form the far more stable ketene. This barrier is high enough that this reaction probably involves e.g.<\/em> biradicals or other pathways.<\/li>\n<\/ol>\n

    \"ro-co1\"<\/a><\/p>\n

    \"ro-co\"<\/a><\/p>\n

    \"ex-co1\"<\/a><\/p>\n

    \"ex-co\"<\/a><\/p>\n

    The question arises how such a CO analogue of diazirines might be made. The very high relative energy does tend to suggest it might have to be a photochemical approach. This would be a challenge, given that photochemistry is also likely to promote CO extrusion. Most likely this species is destined to join the (increasing) collection of molecules known to science only by their computed properties!\u00a0<\/p>\n

    \n

    \u2021<\/sup>Such connectedness in human knowledge has been termed intertwingularity<\/a>\u00a0by Ted Nelson.<\/p>\n

    \u2020<\/sup>Scifinder by and large only abstracts\u00a0articles published in journals, along with some of the data found there. Most calculations never make it to such articles. The newly topical area of Research Data Management<\/em> strives to put in place an infrastructure that addresses such issues.[11]<\/a><\/span><\/p>\n

    \n

    References<\/h2>\n
    1. G.M.S. Yip, Z. Chen, C.J. Edge, E.H. Smith, R. Dickinson, E. Hohenester, R.R. Townsend, K. Fuchs, W. Sieghart, A.S. Evers, and N.P. Franks, \"A propofol binding site on mammalian GABAA receptors identified by photolabeling\", Nature Chemical Biology<\/i>, vol. 9, pp. 715-720, 2013. https:\/\/doi.org\/10.1038\/nchembio.1340<\/a>\n\n<\/li>\n
    2. L. Dubinsky, B.P. Krom, and M.M. Meijler, \"Diazirine based photoaffinity labeling\", Bioorganic & Medicinal Chemistry<\/i>, vol. 20, pp. 554-570, 2012. https:\/\/doi.org\/10.1016\/j.bmc.2011.06.066<\/a>\n\n<\/li>\n
    3. R. Motterlini, and L.E. Otterbein, \"The therapeutic potential of carbon monoxide\", Nature Reviews Drug Discovery<\/i>, vol. 9, pp. 728-743, 2010. https:\/\/doi.org\/10.1038\/nrd3228<\/a>\n\n<\/li>\n
    4. H.S. Rzepa, \"C 2 H 1 F 3 N 2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191529<\/a>\n\n<\/li>\n
    5. H.S. Rzepa, \"C 2 H 1 F 3 N 2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191530<\/a>\n\n<\/li>\n
    6. H.S. Rzepa, \"C2HF3N2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191534<\/a>\n\n<\/li>\n
    7. H.S. Rzepa, \"C 3 H 1 F 3 O 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/191531<\/a>\n\n<\/li>\n
    8. H.S. Rzepa, \"C 3 H 1 F 3 O 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/191535<\/a>\n\n<\/li>\n
    9. H.S. Rzepa, \"C3HF3O\", 2015. https:\/\/doi.org\/10.14469\/ch\/191532<\/a>\n\n<\/li>\n
    10. H.S. Rzepa, \"C3HF3O\", 2015. https:\/\/doi.org\/10.14469\/ch\/191533<\/a>\n\n<\/li>\n
    11. H. Rzepa, \"Workshop presentation on Research Data Management at Imperial College London, 29th September, 2015.\", 2015. https:\/\/doi.org\/10.14469\/hpc\/143<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      How does an anaesthetic work? Surprisingly, it is only recently that the possible binding sites of the anaesthetic propofol (2,6-di-isopropylphenol) have been identified using a technique known as photoaffinity labelling. A propofol analogue was constructed by replacing one of\u00a0the isopropyl groups with a trifluoromethyl diazirine group (R=CF3, X=Y=N below). Upon photolysis, this species looses nitrogen […]<\/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":[4,1086],"tags":[1575,1580,1579,1577,1576],"ppma_author":[2661],"class_list":["post-14575","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","category-reaction-mechanism-2","tag-anaesthetic","tag-diazirine","tag-gabaa-receptors","tag-photo-affinity-labelling","tag-propofol"],"yoast_head":"\nIsoelectronic games: the CO analogue of diazirines as an intriguing species? - 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=14575\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Isoelectronic games: the CO analogue of diazirines as an intriguing species? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"How does an anaesthetic work? Surprisingly, it is only recently that the possible binding sites of the anaesthetic propofol (2,6-di-isopropylphenol) have been identified using a technique known as photoaffinity labelling. A propofol analogue was constructed by replacing one of\u00a0the isopropyl groups with a trifluoromethyl diazirine group (R=CF3, X=Y=N below). Upon photolysis, this species looses nitrogen […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-09-24T13:10:05+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2015-09-25T15:01:46+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/diazirene.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":"Isoelectronic games: the CO analogue of diazirines as an intriguing species? - 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=14575","og_locale":"en_GB","og_type":"article","og_title":"Isoelectronic games: the CO analogue of diazirines as an intriguing species? - Henry Rzepa's Blog","og_description":"How does an anaesthetic work? Surprisingly, it is only recently that the possible binding sites of the anaesthetic propofol (2,6-di-isopropylphenol) have been identified using a technique known as photoaffinity labelling. A propofol analogue was constructed by replacing one of\u00a0the isopropyl groups with a trifluoromethyl diazirine group (R=CF3, X=Y=N below). Upon photolysis, this species looses nitrogen […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575","og_site_name":"Henry Rzepa's Blog","article_published_time":"2015-09-24T13:10:05+00:00","article_modified_time":"2015-09-25T15:01:46+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/diazirene.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=14575#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Isoelectronic games: the CO analogue of diazirines as an intriguing species?","datePublished":"2015-09-24T13:10:05+00:00","dateModified":"2015-09-25T15:01:46+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575"},"wordCount":615,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/diazirene.svg","keywords":["anaesthetic","Diazirine","GABAA receptors","photo affinity labelling","propofol"],"articleSection":["Interesting chemistry","reaction mechanism"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14575","name":"Isoelectronic games: the CO analogue of diazirines as an intriguing species? 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For example, this article has an SI which is paginated at 907; almost a mini-database in its own right!\u2020\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":12261,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12261","url_meta":{"origin":14575,"position":1},"title":"A connected world (journals and blogs): The benzene dication.","author":"Henry Rzepa","date":"April 10, 2014","format":false,"excerpt":"Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":17142,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17142","url_meta":{"origin":14575,"position":2},"title":"Molecule of the year (month\/week)?","author":"Henry Rzepa","date":"December 12, 2016","format":false,"excerpt":"Chemical and engineering news (C&EN) is asking people to vote for their molecule of the year from six highlighted candidates. This reminded me of the history of internet-based \"molecules of the moment\". It is thought that the concept originated in December 1995 here at Imperial and in January 1996 at\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\/2016\/12\/ferris.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":10733,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10733","url_meta":{"origin":14575,"position":3},"title":"Is dicarbon (C2) a molecule of chemical interest?","author":"Henry Rzepa","date":"July 3, 2013","format":false,"excerpt":"C2\u00a0(dicarbon) is certainly interesting from a theoretical point of view. Whether or not it can be described as having a quadruple bond has induced much passionate discussion,,,. Its occurrence in space and in flames is also well-known. But does it have what might be called a conventional chemistry? Other highly\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":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/LaOsC1.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23240,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23240","url_meta":{"origin":14575,"position":4},"title":"The chemical synthesis of C2: another fascinating twist to the story.","author":"Henry Rzepa","date":"January 20, 2021","format":false,"excerpt":"Last May, I wrote an update to the story sparked by the report of the chemical synthesis of C2. This species has a long history of spectroscopic observation in the gas phase, resulting from its generation at high temperatures. The chemical synthesis however was done in solution at ambient or\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\/2021\/01\/11-dim.gif?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/01\/11-dim.gif?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/01\/11-dim.gif?resize=525%2C300&ssl=1 1.5x"},"classes":[]},{"id":17763,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17763","url_meta":{"origin":14575,"position":5},"title":"Peroxydisulfate – “enables a non-enzymatic Krebs cycle precursor”","author":"Henry Rzepa","date":"March 19, 2017","format":false,"excerpt":"The Wikipedia entry on peroxydisulfate is quite short (as of today). But I suspect this article may change things.. A search of the Cambridge structure database reveals around 18 high quality crystal structures containing this species are known, many as metal salts. The article reports that \"in the presence of\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\/157-1024x364.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\/14575","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=14575"}],"version-history":[{"count":20,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14575\/revisions"}],"predecessor-version":[{"id":14600,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14575\/revisions\/14600"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14575"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14575"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14575"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14575"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}