{"id":10220,"date":"2013-04-17T08:59:29","date_gmt":"2013-04-17T07:59:29","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10220"},"modified":"2014-01-17T07:42:55","modified_gmt":"2014-01-17T07:42:55","slug":"x-ray-analysis-and-absolute-configuration-determination-using-porous-complexes","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10220","title":{"rendered":"X-ray analysis and absolute configuration determination using porous complexes."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"10220\">\n<p>This is another in the occasional series of &#8220;what a neat molecule&#8221;. In this case, more of a &#8220;what a neat idea&#8221;. The s-triazine below, when coordinated to eg ZnI<sub>2<\/sub>, forms what is called a metal-organic-framework, or MOF. A recent article<span id=\"cite_ITEM-10220-0\" name=\"citation\"><a href=\"#ITEM-10220-0\">[1]<\/a><\/span> shows how such frameworks can be used to help solve a long-standing problem in structure determination, how to get a crystal structure on a compound that does not crystallise on its own.<\/p>\n<p>&nbsp;<\/p>\n<p><img decoding=\"async\" class=\"aligncenter size-full wp-image-10221\" alt=\"MOF\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/MOF1.svg\" width=\"300\" \/><\/p>\n<p>The essence of the technique is to select a small crystal of the MOF (which crystallises well) and allow your own molecule to diffuse in from solution. So captured inside the framework, the X-ray analysis can now be done on the absorbed host molecule together with the MOF framework. Below you can see two of the structures reported solved by this technique. The first shows the target molecule (green arrows) but also three molecules of cyclohexane (the diffusing solvent, red arrows), nicely illustrating its chair conformation.<\/p>\n<div id=\"attachment_10223\" style=\"width: 430px\" class=\"wp-caption aligncenter\"><img decoding=\"async\" aria-describedby=\"caption-attachment-10223\" class=\"size-full wp-image-10223\" onclick=\"jmolInitialize('..\/Jmol\/','JmolAppletSigned.jar');jmolSetAppletColor('white');jmolApplet([1000,1000],'load wp-content\/uploads\/2013\/04\/p21.cif;zoom 10;moveto 4 0 2 0 90 95;');\" alt=\"Click for  3D.\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/910394.jpeg\" width=\"420\" \/><p id=\"caption-attachment-10223\" class=\"wp-caption-text\">Click for 3D.<\/p><\/div>\n<p>This second example shows the structure of a marine natural product, of which only \u00a0about 5\u00b5g was available (green arrow). The structure (of <strong>miyakosyne A<\/strong>) shows a conformationally flexible substituted saturated backbone, a molecule which traditionally might be expected to be disordered because of its flexibility. These structures were performed on a standard diffractometer, and the authors point out that if more intense synchrotron radiation were to be used, even smaller samples (< 10ng) could be determined. They also note that full occupancy of the MOF lattice does not need to be achieved for the method to succeed.<\/p>\n<\/p>\n<div id=\"attachment_10229\" style=\"width: 430px\" class=\"wp-caption aligncenter\"><img decoding=\"async\" aria-describedby=\"caption-attachment-10229\" class=\"size-full wp-image-10229\" onclick=\"jmolInitialize('..\/Jmol\/','JmolAppletSigned.jar');jmolSetAppletColor('white');jmolApplet([1000,1000],'load wp-content\/uploads\/2013\/04\/c2-sr.cif;zoom 10;moveto 4 0 2 0 90 95;');\" alt=\"Click fdx.doi.org3D.\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/np.jpeg\" width=\"420\" \/><p id=\"caption-attachment-10229\" class=\"wp-caption-text\">Click for 3D.<\/p><\/div>\n<p>I end with noting that in an earlier post, I observed how chiroptical methods can nowadays be increasingly successfully used to determine absolute configurations of chiral molecules. Miyakosyne A, a molecule with three chiral centres had proved to be a challenge using such techniques; one of these centres (at C14) could not be determined by any chiroptical method. The configuration was however successfully determined as (S) by this new crystallographic technique. I think this is a huge contribution to the science of structure and configuration determination!<span id=\"cite_ITEM-10220-1\" name=\"citation\"><a href=\"#ITEM-10220-1\">[2]<\/a><\/span><\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-10220-0\">Y. Inokuma, S. Yoshioka, J. Ariyoshi, T. Arai, Y. Hitora, K. Takada, S. Matsunaga, K. Rissanen, and M. Fujita, \"X-ray analysis on the nanogram to microgram scale using porous complexes\", <i>Nature<\/i>, vol. 495, pp. 461-466, 2013. <a href=\"https:\/\/doi.org\/10.1038\/nature11990\">https:\/\/doi.org\/10.1038\/nature11990<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 10220 -->","protected":false},"excerpt":{"rendered":"<p>This is another in the occasional series of &#8220;what a neat molecule&#8221;. In this case, more of a &#8220;what a neat idea&#8221;. The s-triazine below, when coordinated to eg ZnI2, forms what is called a metal-organic-framework, or MOF. A recent article shows how such frameworks can be used to help solve a long-standing problem in [&hellip;]<\/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":[48,1041,157,1042,42],"ppma_author":[2661],"class_list":["post-10220","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-chair","tag-marine-natural-product","tag-metal","tag-radiation","tag-x-ray"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>X-ray analysis and absolute configuration determination using porous complexes. - Henry Rzepa&#039;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=10220\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"X-ray analysis and absolute configuration determination using porous complexes. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"This is another in the occasional series of &#8220;what a neat molecule&#8221;. In this case, more of a &#8220;what a neat idea&#8221;. The s-triazine below, when coordinated to eg ZnI2, forms what is called a metal-organic-framework, or MOF. A recent article shows how such frameworks can be used to help solve a long-standing problem in [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10220\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-04-17T07:59:29+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2014-01-17T07:42:55+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/MOF1.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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"X-ray analysis and absolute configuration determination using porous complexes. - Henry Rzepa&#039;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=10220","og_locale":"en_GB","og_type":"article","og_title":"X-ray analysis and absolute configuration determination using porous complexes. - Henry Rzepa&#039;s Blog","og_description":"This is another in the occasional series of &#8220;what a neat molecule&#8221;. 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Thus \"NU-1501-Al\" can absorb 14 weight% of hydrogen. To power a low-polluting car with a 500 km range, about\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","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\/04\/MOF1-1024x990.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":275,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=275","url_meta":{"origin":10220,"position":1},"title":"A molecule with an identity crisis: Aromatic or anti-aromatic?","author":"Henry Rzepa","date":"April 13, 2009","format":false,"excerpt":"In 1988, Wilke reported molecule 1 It was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned! The reason is that a\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"A [24] annulene. Click on image for model.","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/gaytab.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":28233,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28233","url_meta":{"origin":10220,"position":2},"title":"Molecules of the Year 2024: Molecular shuttle in a box.","author":"Henry Rzepa","date":"January 25, 2025","format":false,"excerpt":"This is another in the C&E News list of candidates for the Molecule of the Year, Molecular shuttle in a box 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 The molecule shown below inside the cavity\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":28187,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28187","url_meta":{"origin":10220,"position":3},"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 &quot;Interesting chemistry&quot;","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":14272,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14272","url_meta":{"origin":10220,"position":4},"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 &quot;Interesting chemistry&quot;","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":11597,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11597","url_meta":{"origin":10220,"position":5},"title":"The subtle effect of dispersion forces on the shapes of molecules:  benzyl magnesium bromide.","author":"Henry Rzepa","date":"November 10, 2013","format":false,"excerpt":"In the previous post I mentioned in passing the Grignard reagent benzyl magnesium bromide as having tetrahedral coordination at Mg. But I have now noticed, largely through spotting Steve Bachrach's post on \"Acene dimers \u2013 open or closed?\" another geometric effect perhaps worthy of note, certainly one not always noted\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/10220","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=10220"}],"version-history":[{"count":13,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10220\/revisions"}],"predecessor-version":[{"id":11936,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10220\/revisions\/11936"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=10220"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=10220"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=10220"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=10220"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}