{"id":4930,"date":"2011-09-20T15:07:29","date_gmt":"2011-09-20T15:07:29","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=4930"},"modified":"2011-09-26T16:09:44","modified_gmt":"2011-09-26T16:09:44","slug":"molecular-matryoshka-dolls","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4930","title":{"rendered":"Molecular Matryoshka dolls"},"content":{"rendered":"
\n

A Matryoshka doll<\/a> is better known as a Russian nesting doll. They can have up to eight layers. Molecules can only emulate two layers, although see here<\/a> for a good candidate for making a three-layered example (the inside layer is C60<\/sub>, which itself might<\/a>\u00a0encapsulate\u00a0a small molecule. See also \u00a0DOI: 10.1021\/ja991747w<\/a>). These molecular dolls can be created out of quite simple molecules. Here I explore just one, and focus on what is happening inside!<\/p>\n

\"\"<\/a>

The basic component of a molecular capsule.<\/p><\/div>\n

The above represents the “tennis ball” component of a molecule first made by Branda, Wyler and Rebek (DOI: 10.1126\/science.8122107<\/a>) in 1994. It has four pairs of carbonyl\/NH units, and two of these molecules can stitch together to form an almost spherical capsule. Into this can pop smaller molecules, and in this case methane was persuaded to enter (highlighted with a magenta arrow below).<\/p>\n

\"\"

A molecular Russian doll with methane inside. Click for 3D<\/p><\/div>Finding out the structure of these dolls can be a tricky business. More often than not, they do not crystallise nicely enough to determine this by X-ray analysis (the structure of this one has never been reported, the structure above is a calculation), and even if the basic container could be analysed, the small molecules inside often rattle around too much (i.e.<\/em> they are disordered) for their optimum position to be identified. Rebek and co resorted to 1<\/sup>H NMR spectroscopy. If you read their paper, you will find that the chemical shift of the four methane protons comes at -0.91 ppm if inside the cavity, and at +0.23 outside. These sorts of induced shifts (they can be very much larger) makes the identification of more complex molecules which may be inside the cavity a fraught business. Is there another method? Here I suggest that the 1<\/sup>H NMR spectrum can be calculated to sufficient accuracy to be able to comment on that internal structure.<\/p>\n

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

The above is a \u03c9B97XD\/6-311G(d,p)\/SCRF=dichloromethane<\/a> calculation (under optimum conditions, this can predict the shifts of protons to an accuracy of < 0.1 ppm!). So it is here, with the calculated methane chemical shift being -0.84 ppm (averaged over the four protons). In fact, the spectrum above is amazingly like the real thing (which can be seen at the DOI above), excepting of course proton couplings. Oh, if you cannot see a spectrum, it is because your browser does not support SVG. Why did I use this format? So that you can expand the view above (zoom in using your browser), and the SVG will rescale the drawing without loss of resolution!<\/p>\n

We might presume then that the calculated structure must be a good model for the real thing (the structure of which Rebek and Co were never able to obtain). If you click on the model above, you may notice that the methane is not located exactly in the centre of the cavity, but it is displaced towards the face of one of the benzene rings, and away from the other. Thus these internal dolls do have a preference for where they sit, a phenomenon by the way which Rebek has termed social <\/em>(molecular) isomerism (DOI:\u00a010.1021\/ja020607a<\/a>).<\/em>This system has 181 atoms. I estimate that this sort of calculation can readily be done for molecules with up to about 250 atoms nowadays, which would cover a fair sprinkling of these molecular Matryoshka dolls.<\/p>\n

Postscript: \u00a0<\/strong>Professor Rebek has kindly sent me the spectrum of both\u00a0encapsulated\u00a0methane and ethane which is reproduced below. The NMR of ethane calculated by the same procedure as above is -0.41 ppm.<\/p>\n

\"\"<\/a>

The 1H NMR spectrum of encapsulated methane and ethane.<\/p><\/div>\n

\n

Archived on 2011-09-26. URL:http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=4930. Accessed: 2011-09-26. (Archived by WebCite\u00ae at http:\/\/www.webcitation.org\/61zSZeG7P<\/a>)<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

A Matryoshka doll is better known as a Russian nesting doll. They can have up to eight layers. Molecules can only emulate two layers, although see here for a good candidate for making a three-layered example (the inside layer is C60, which itself might\u00a0encapsulate\u00a0a small molecule. See also \u00a0DOI: 10.1021\/ja991747w). These molecular dolls can be […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1,4],"tags":[],"ppma_author":[2661],"class_list":["post-4930","post","type-post","status-publish","format-standard","hentry","category-general","category-interesting-chemistry"],"yoast_head":"\nMolecular Matryoshka dolls - 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=4930\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Molecular Matryoshka dolls - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"A Matryoshka doll is better known as a Russian nesting doll. They can have up to eight layers. Molecules can only emulate two layers, although see here for a good candidate for making a three-layered example (the inside layer is C60, which itself might\u00a0encapsulate\u00a0a small molecule. See also \u00a0DOI: 10.1021\/ja991747w). These molecular dolls can be […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4930\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-09-20T15:07:29+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-09-26T16:09:44+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/rebek.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":"Molecular Matryoshka dolls - 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=4930","og_locale":"en_GB","og_type":"article","og_title":"Molecular Matryoshka dolls - Henry Rzepa's Blog","og_description":"A Matryoshka doll is better known as a Russian nesting doll. They can have up to eight layers. Molecules can only emulate two layers, although see here for a good candidate for making a three-layered example (the inside layer is C60, which itself might\u00a0encapsulate\u00a0a small molecule. See also \u00a0DOI: 10.1021\/ja991747w). 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It is an annulene with 144 all-cis CH groups, being a (very) much larger cousin of (also hypothetical) systems mooted in 2009,. One fascinating novel aspect of Berger's work is\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":"A 144-carbon annulene. Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/C144.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":3472,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3472","url_meta":{"origin":4930,"position":1},"title":"A short history of molecular modelling: 1860-1890.","author":"Henry Rzepa","date":"February 5, 2011","format":false,"excerpt":"In 1953, the model of the DNA molecule\u00a0led to what has become regarded as the most\u00a0famous scientific diagram\u00a0of the 20th century. It had all started 93 years earlier in\u00a01860, at a time when the tetravalency of carbon was only just established (by William Odling) and the concept of atoms as\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/02\/molmod.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24027,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24027","url_meta":{"origin":4930,"position":2},"title":"Molecules with very large dipole moments: cyclopropenium acetylide","author":"Henry Rzepa","date":"July 11, 2021","format":false,"excerpt":"Occasionally, someone comments about an old post here, asking a question. Such was the case here, when a question about the dipole moment of cyclopropenylidene arose. It turned out to be 3.5D, but this question sparked a thought about the related molecule below. Of the two resonance forms show above,\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\/07\/C5H5-esp-1024x690.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":17771,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17771","url_meta":{"origin":4930,"position":3},"title":"Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism.","author":"Henry Rzepa","date":"March 20, 2017","format":false,"excerpt":"The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate\u00a0(IRC). Here I explore an alternative method based instead on computing a molecular\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":"","width":0,"height":0},"classes":[]},{"id":12978,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12978","url_meta":{"origin":4930,"position":4},"title":"WATOC2014 Conference report. Emergent themes.","author":"Henry Rzepa","date":"October 9, 2014","format":false,"excerpt":"This second report highlights two \"themes\", or common ideas that seem to emerge spontaneously from diversely different talks. Most conferences do have them. The first is \"embedding\", which in this context means treating different parts of a probably complex molecular system at different levels of theory. Thus Emily Carter in\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":10990,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10990","url_meta":{"origin":4930,"position":5},"title":"Molecule-sized pixels.","author":"Henry Rzepa","date":"August 11, 2013","format":false,"excerpt":"The ultimate reduction in size for an engineer is to a single molecule. It's been done for a car; now it has been reported for the pixel (picture-element). The molecule above (X=O, NR, R=aryl, etc) has been shown to be capable of acting as a molecular pixel. To give some\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\/4930","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=4930"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4930\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4930"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4930"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4930"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=4930"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}