{"id":23111,"date":"2020-12-30T18:15:00","date_gmt":"2020-12-30T18:15:00","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=23111"},"modified":"2020-12-30T18:26:24","modified_gmt":"2020-12-30T18:26:24","slug":"tying-different-knots-in-a-molecular-strand","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23111","title":{"rendered":"Tying different knots in a molecular strand."},"content":{"rendered":"
\n

The title derives from an article[1]<\/a><\/span> which was shortlisted for the annual c&en molecule of the year 2020 awards<\/a> (and which I occasionally cover here). In fact this year’s overall theme is certainly large molecules, the one exception being a smaller molecule with a quadruple bond to boron, a theme I have already covered here.<\/a><\/p>\n

To illustrate a main theme of many of these award-winning molecules, I often look to showing either a computed property (such as each of the localised orbitals for the quadruple bond to boron) or the actual 3D coordinates. In this example, they were there in the supporting information and are presented here as rotatable 3D models without any further transformation. The authors of the article encourage the reader to spot the different types of knot that can be tied in the three molecules reported, but to show how difficult it can be to get a good perception of this, I illustrate the standard journal presentation of a static 2D projection of the 3D structure. It can be a nightmare to try to find the optimum such projection for larger molecules and so often they are reduced to much simpler schematics to get the message across. Well, below you can see three (unoptimized) projections, but you can covert them to 3D form by clicking on the scheme and then select your own projection.<\/p>\n

\"\"

(52)-1-CuLu<\/p><\/div>\n

\"\"

(52)-L1-CuLu<\/p><\/div>\n

\"\"

(52)-1-CuLu<\/p><\/div>\n

Synthesized molecules with knots and the like have been around since about 1967, but they have certainly come on a pace since then. It would be interesting to see if any have properties unique to knots that have seen spectacular uses!<\/p>\n

References<\/h2>\n
  1. D.A. Leigh, F. Schaufelberger, L. Pirvu, J.H. Stenlid, D.P. August, and J. Segard, \"Tying different knots in a molecular strand\", Nature<\/i>, vol. 584, pp. 562-568, 2020. https:\/\/doi.org\/10.1038\/s41586-020-2614-0<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    The title derives from an article which was shortlisted for the annual c&en molecule of the year 2020 awards (and which I occasionally cover here). In fact this year’s overall theme is certainly large molecules, the one exception being a smaller molecule with a quadruple bond to boron, a theme I have already covered here. […]<\/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-23111","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nTying different knots in a molecular strand. - 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=23111\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tying different knots in a molecular strand. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The title derives from an article which was shortlisted for the annual c&en molecule of the year 2020 awards (and which I occasionally cover here). In fact this year’s overall theme is certainly large molecules, the one exception being a smaller molecule with a quadruple bond to boron, a theme I have already covered here. […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23111\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2020-12-30T18:15:00+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2020-12-30T18:26:24+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/12\/51-L1-CuLu.jpg\" \/>\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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Tying different knots in a molecular strand. - 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=23111","og_locale":"en_GB","og_type":"article","og_title":"Tying different knots in a molecular strand. - Henry Rzepa's Blog","og_description":"The title derives from an article which was shortlisted for the annual c&en molecule of the year 2020 awards (and which I occasionally cover here). 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I had previously mooted that the Fe\u2a78C combination might be\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\/2021\/05\/Screenshot-703-1024x818.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":23777,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23777","url_meta":{"origin":23111,"position":1},"title":"A suggestion for a molecule with a M\u2a78C quadruple bond with trigonal metal coordination.","author":"Henry Rzepa","date":"May 13, 2021","format":false,"excerpt":"The proposed identification of molecules with potential metal to carbon quadruple bonds, in which the metal exhibits trigonal bipyramidal coordination rather than the tetrahedral modes which have been proposed in the literature,, leads on to asking whether simple trigonal coordination at the metal can also sustain this theme? The rational\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":23588,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23588","url_meta":{"origin":23111,"position":2},"title":"Two new reality-based suggestions for molecules with a metal M\u2a78C quadruple bond.","author":"Henry Rzepa","date":"May 8, 2021","format":false,"excerpt":"Following from much discussion over the last decade about the nature of C2, a diatomic molecule which some have suggested sustains a quadruple bond between the two carbon atoms, new ideas are now appearing for molecules in which such a bond may also exist between carbon and a transition metal\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\/2021\/05\/Screenshot-702-300x63.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":21846,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21846","url_meta":{"origin":23111,"position":3},"title":"Comment on “Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces”: The 7\u03a3 heptet excited states for related molecules.","author":"Henry Rzepa","date":"January 2, 2020","format":false,"excerpt":"I noted in an earlier blog, a potential (if difficult) experimental test of the properties of the singlet state of dicarbon, C2. Now, just a few days ago, a ChemRxiv article has been published suggesting another (probably much more realistic) test.\u00a0This looks at the so-called 7\u03a3 open shell state of\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\/2020\/01\/checkpoint_10062095-300x169.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":22971,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22971","url_meta":{"origin":23111,"position":4},"title":"A new example of a quadruple bond from carbon – to Fe.","author":"Henry Rzepa","date":"November 7, 2020","format":false,"excerpt":"Way back in 2010, I was writing about an experience I had just had during an organic chemistry tutorial, which morphed into speculation as to whether a carbon atom might sustain a quadruple bond to nitrogen. A decade on, and possibly approaching 100 articles by many authors on the topic,\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\/2020\/11\/NMn_33a-1024x839.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":14272,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14272","url_meta":{"origin":23111,"position":5},"title":"Electrides (aka solvated electrons).","author":"Henry Rzepa","date":"July 8, 2015","format":false,"excerpt":"Peter Edwards has just given the 2015 Hofmann lecture here at Imperial on the topic of solvated electrons. An organic chemist knows this species as \"e-\" and it occurs in ionic compounds known as electrides; chloride = the negative anion of a chlorine atom, hence electride = the negative anion\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":[]}],"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\/23111","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=23111"}],"version-history":[{"count":16,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/23111\/revisions"}],"predecessor-version":[{"id":23133,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/23111\/revisions\/23133"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23111"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23111"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23111"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=23111"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}