{"id":14548,"date":"2015-09-06T11:31:12","date_gmt":"2015-09-06T10:31:12","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14548"},"modified":"2023-09-17T07:20:47","modified_gmt":"2023-09-17T06:20:47","slug":"deviations-from-tetrahedral-four-coordinate-carbon-a-statistical-exploration","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548","title":{"rendered":"Deviations from tetrahedral four-coordinate carbon: a statistical exploration."},"content":{"rendered":"
\n

\n\tAn article entitled "Four Decades of the Chemistry of Planar Hypercoordinate Compounds<\/em>"[1]<\/a><\/span> was recently reviewed<\/a> by Steve Bacharach on his blog, where you can also see comments<\/a>. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate carbon.\n<\/p>\n

\n\tThe search definition is shown below using a  simple carbon with four ligands,‡<\/sup> the ligands themselves also being tetracoordinate carbon. The search is restricted to data collected below temperatures of 140K, as well as R-factor <5%, no errors and no disorder. Cyclic species are allowed and a statistically reasonable 2773 hits emerged from the search.\n<\/p>\n

\n\t\"Scheme\"\n<\/p>\n

\n\tRecollect that the idealised angle subtended at the centre is 109.47°. I show below three separate heat plots of the search results. Why three? The way the search software (Conquest) works is that one could define four C-C distances and six angles, and then plot any combination of one distance and one angle. I show just three combinations here, but could have included many more.\n<\/p>\n

\n\tThere appear to be four distinct clusters of values for this angle that emerge from the three plots shown below (the "bin size" is 100, and the frequency colour code indicates how many hits there are in each bin).\n<\/p>\n

    \n
  1. \n\t\tThe hotspot is unsurprisingly ~109° with a corresponding C-C distance of ~1.54Å.\n\t<\/li>\n
  2. \n\t\tThere may be two clusters at angles of ~60° (cyclopropane), with C-C values ranging from ~1.47 to ~1.55Å.\n\t<\/li>\n
  3. \n\t\tA collection at ~90° (mostly cyclobutane?), with C-C values up to 1.6Å.\n\t<\/li>\n
  4. \n\t\tA collection at ~140° (again small rings), now with much shorter C-C values of ~1.46Å. This reminds of the approximation that the hybridisation in e.g.<\/em> cyclopropane is a combination of sp5<\/sup> and sp3<\/sup>.\n\t<\/li>\n<\/ol>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n\tIdeally, what one might want to plot would be sums of four angles; for a pure tetrahedral carbon the sum would always be 438° (4*109.47°) but for a pure planar carbon it could be as low as 360° (4*90°). One could then see how closely the distribution approaches to the latter and hence reveal whether there are any true planar tetracoordinate carbon species known. Although the Conquest software cannot analyse in such terms, a Python-based API<\/a> has recently been released that should allow this to be done, although I should state that this requires a commercial license and it is not open access code. If we manage to get it working, I will report!\n<\/p>\n

    \n

    \n\t‡<\/sup>As a teaser I also include a plot of six-coordinate carbon, in which the ligands can be any non-metal. Note the clusters at angles of 60, ~112 and ~120-130°. It is worth pointing out that the definition of the connection between a carbon and a ligand as a "bond" becomes increasingly arbitrary as the coordination becomes "hyper". Because crystallography does not measure electron densities in "bonds", we know nothing of its topology in this region. It is therefore quite possible that the appearance of the heat plot below might be related just as much to whatever convention is being used in creating the entry in the CSD as it would be to a quantum analysis of the bonding.\n<\/p>\n

    \n\t\"Scheme\"\n<\/p>\n

    \n

    Acknowledgments<\/h4>\n

    This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n

    References<\/h2>\n
    1. L. Yang, E. Ganz, Z. Chen, Z. Wang, and P.V.R. Schleyer, \"Four Decades of the Chemistry of Planar Hypercoordinate Compounds\", Angewandte Chemie International Edition<\/i>, vol. 54, pp. 9468-9501, 2015. https:\/\/doi.org\/10.1002\/anie.201410407<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      An article entitled "Four Decades of the Chemistry of Planar Hypercoordinate Compounds" was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate […]<\/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":[2,1745],"tags":[1553,144,557,1550,1551,78,1549,1552,157,1001,996,1554,1555],"ppma_author":[2661],"class_list":["post-14548","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-angle","tag-cambridge","tag-chemical-bonding","tag-cycloalkane","tag-cyclopropane","tag-html","tag-html-element","tag-ligand","tag-metal","tag-search-definition","tag-search-results","tag-search-software","tag-steve-bacharach"],"yoast_head":"\nDeviations from tetrahedral four-coordinate carbon: a statistical exploration. - 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=14548\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Deviations from tetrahedral four-coordinate carbon: a statistical exploration. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"An article entitled "Four Decades of the Chemistry of Planar Hypercoordinate Compounds" was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-09-06T10:31:12+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-17T06:20:47+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC.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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Deviations from tetrahedral four-coordinate carbon: a statistical exploration. - 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=14548","og_locale":"en_GB","og_type":"article","og_title":"Deviations from tetrahedral four-coordinate carbon: a statistical exploration. - Henry Rzepa's Blog","og_description":"An article entitled "Four Decades of the Chemistry of Planar Hypercoordinate Compounds" was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548","og_site_name":"Henry Rzepa's Blog","article_published_time":"2015-09-06T10:31:12+00:00","article_modified_time":"2023-09-17T06:20:47+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC.jpg","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=14548#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Deviations from tetrahedral four-coordinate carbon: a statistical exploration.","datePublished":"2015-09-06T10:31:12+00:00","dateModified":"2023-09-17T06:20:47+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548"},"wordCount":558,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/09\/CC.jpg","keywords":["Angle","Cambridge","chemical bonding","Cycloalkane","Cyclopropane","HTML","HTML element","Ligand","metal","search definition","search results","search software","Steve Bacharach"],"articleSection":["Chemical IT","crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548","name":"Deviations from tetrahedral four-coordinate carbon: a statistical exploration. - 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So what does a search for this situation reveal in the CSD? The query can be\u2026","rel":"","context":"With 2 comments","block_context":{"text":"With 2 comments","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25581#comments"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/111-nbo.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":17805,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17805","url_meta":{"origin":14548,"position":1},"title":"Silyl cations?","author":"Henry Rzepa","date":"March 23, 2017","format":false,"excerpt":"It is not only the non-classical norbornyl cation that has proved controversial in the past. A colleague mentioned at lunch (thanks Paul!) that tri-coordinate group 14 cations such as R3Si+ have also had an interesting history. Here I take a brief look at some of these systems. Their initial characterisations,\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\/164-1024x748.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":28187,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28187","url_meta":{"origin":14548,"position":2},"title":"Molecules of the Year 2024: A crystal structure perspective on anti-Bredt olefins.","author":"Henry Rzepa","date":"January 8, 2025","format":false,"excerpt":"Each year C&E News publishes a list of candidates for the Molecule of the Year. For 2024 the list is (in order of votes cast for each) Mirror-image cyclodextrin Molecular shuttle in a box Rule-bending strained alkene First soluble promethium complex Single-electron carbon-carbon bond Hot MOF for capturing carbon I\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":21883,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21883","url_meta":{"origin":14548,"position":3},"title":"Molecules of the year 2019: Hexagonal planar crystal structures.","author":"Henry Rzepa","date":"January 23, 2020","format":false,"excerpt":"Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. This was a mode of metal coordination first mooted more than 100 years ago, but with the first examples only being discovered recently.\u00a0The C&E News example comprises a central\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\/2020\/01\/norloy-300x263.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":14560,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560","url_meta":{"origin":14548,"position":4},"title":"Deviations from planarity of trigonal carbon and from linearity of digonal carbon.","author":"Henry Rzepa","date":"September 13, 2015","format":false,"excerpt":"Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons.\u00a0 Firstly, the digonal C\u2261C case. Attached to each carbon of the C\u2261C unit are two saturated carbon ligands;\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":845,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=845","url_meta":{"origin":14548,"position":5},"title":"It’s penta-coordinate carbon Spock- but not as we know it!","author":"Henry Rzepa","date":"September 30, 2009","format":false,"excerpt":"In the previous two posts, I noted the recent suggestion of how a stable frozen SN2 transition state might be made. This is characterised by a central carbon with five coordinated ligands. The original suggestion included two astatine atoms as ligands (X=At), but in my post I suggested an alternative\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The Sn2 transition state","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/sn2.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\/14548","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=14548"}],"version-history":[{"count":10,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14548\/revisions"}],"predecessor-version":[{"id":26497,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14548\/revisions\/26497"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14548"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14548"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14548"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14548"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}