{"id":27476,"date":"2024-08-26T10:53:28","date_gmt":"2024-08-26T09:53:28","guid":{"rendered":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27476"},"modified":"2024-09-04T10:47:36","modified_gmt":"2024-09-04T09:47:36","slug":"mechanism-of-the-masamune-bergman-reaction-part-2-a-possible-3d-model-for-calicheamicin-revealing-the-non-covalent-interactions-nci-present","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27476","title":{"rendered":"Mechanism of the Masamune-Bergman reaction. Part 2: a possible 3D Model for Calicheamicin revealing the non-covalent-interactions (NCI) present."},"content":{"rendered":"
\n

Calicheamicin<\/a> is a natural product with antitumour properties discovered in the 1980s, with the structure shown below. As noted elsewhere<\/a>, this structure has many weird properties, including amongst other features an unusual “enedidyne” motif and the presence of an iodo group on an aromatic ring. Its\u00a0isolated 3D structure is quite difficult to get hold of (embedded structures in a DNA fragment are available however);\u00a0the 3D model associated with the Wikipedia entry\u00a0is essentially only in 2D. The representation shown below, including the absolute stereochemistry, was obtained from the SciFinder entry. <\/p>\n

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

As a prelude to modelling the mechanism of the Bergman cyclisation (for Part 1 in which a simple cycloendiyne is explored, see DOI: 10.59350\/jczra-f0r90<\/a> [1]<\/a><\/span>) of the enediyne ring on this actual molecule, a 3D model was constructed.\u2021<\/sup> One possible such model is shown below,\u00a0built to maximise wherever possible interactions such as hydrogen bonds and weak dispersion attractions from eg methyl groups.\u00a0A side benefit of doing this is the natural emergence of a “cavity” in which the very large iodine atoms snuggles, as it happens adjacent to the enediyne component – something you would not naturally infer from the structure representation shown above! A spacefill model of this conformation is shown below (click on the image to get an interactive version), emerging from an \u03c9B97XD\/Def2-SVPP energy minimisation (DOI: 10.14469\/hpc\/14586<\/a>).[2]<\/a><\/span><\/p>\n

\"\"<\/p>\n

The below shows a crystal structure (2pik<\/a>) of Calicheamicin embedded into a DNA duplex,†<\/sup> which shows a stretched linear conformation of Calicheamicin rather than the compact form more appropriate for an isolated molecule.<\/p>\n

\"\"<\/p>\n

The next step was to use the \u03c9B97XD\/Def2-SVPP wavefunction[2]<\/a><\/span> to calculate the full electron density for the molecule, and using this to evaluate the NCI (non-covalent-interaction) isosurfaces. These are shown below, and the eye is immediately drawn to the regions surrounding that iodine atom, which are replete with attractive green surfaces. Blue and cyan coloured surfaces derive from hydrogen bonds formed within the\u00a03D structure (click on the image to get an interactive version, but be patient, it takes a little while to load). <\/p>\n

\"\"<\/p>\n

The next stage, using the model to evaluate the energetics of the Masamune-Bergman cyclisation for Calicheamicin itself will be reported in part 3.<\/p>\n

\n

\u2021<\/sup>For those interested, this was constructed in stages. The structure representation had been drawn in\u00a0Chemdraw, saved as a pseudo 3D molfile and then loaded into Gaussview. There, it was subjected to several cycles of energy minimisation using the MMFF94 molecular mechanics force field.\u00a0The stereochemistry of all the centres was carefully checked at each stage, if necessary corrected and re-optimised. The next stage was to subject it to a PM7 semiempirical SCF minimisation, a method which includes dispersion attraction terms and which\u00a0tends to give\u00a0geometries that are quite close to eg those obtained using dispersion-corrected DFT methods, in this example \u03c9B97XD\/Def2-SVPP.<\/p>\n

\n

<\/p>\n

<\/p>\n

References<\/h2>\n
  1. H. Rzepa, \"Mechanism of the Masamune-Bergman reaction. Part 1.\", 2024. https:\/\/doi.org\/10.59350\/jczra-f0r90<\/a>\n\n<\/li>\n
  2. H. Rzepa, \"Calicheamicin, full system, reactant, wB97XD\/Def2-svpp G = -5768.785232\", 2024. https:\/\/doi.org\/10.14469\/hpc\/14586<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Calicheamicin is a natural product with antitumour properties discovered in the 1980s, with the structure shown below. As noted elsewhere, this structure has many weird properties, including amongst other features an unusual “enedidyne” motif and the presence of an iodo group on an aromatic ring. Its\u00a0isolated 3D structure is quite difficult to get hold of […]<\/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],"tags":[],"ppma_author":[2661],"class_list":["post-27476","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nMechanism of the Masamune-Bergman reaction. Part 2: a possible 3D Model for Calicheamicin revealing the non-covalent-interactions (NCI) present. - 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=27476\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Mechanism of the Masamune-Bergman reaction. Part 2: a possible 3D Model for Calicheamicin revealing the non-covalent-interactions (NCI) present. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Calicheamicin is a natural product with antitumour properties discovered in the 1980s, with the structure shown below. As noted elsewhere, this structure has many weird properties, including amongst other features an unusual “enedidyne” motif and the presence of an iodo group on an aromatic ring. Its\u00a0isolated 3D structure is quite difficult to get hold of […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27476\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2024-08-26T09:53:28+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-09-04T09:47:36+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/08\/Calicheamicin.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=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Mechanism of the Masamune-Bergman reaction. 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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","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\/27476","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=27476"}],"version-history":[{"count":129,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/27476\/revisions"}],"predecessor-version":[{"id":27708,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/27476\/revisions\/27708"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=27476"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=27476"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=27476"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=27476"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}