{"id":16997,"date":"2016-10-16T08:49:55","date_gmt":"2016-10-16T07:49:55","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16997"},"modified":"2016-10-16T18:03:29","modified_gmt":"2016-10-16T17:03:29","slug":"an-inorganic-double-helix-snip","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16997","title":{"rendered":"An inorganic double helix: SnIP."},"content":{"rendered":"
\n
After sixty years of searching, the first non-templated double helical carbon-free inorganic molecular structure has been reported.[1]<\/a><\/span> That is so neat that I thought to load the 3D coordinates here for you to interact with\u00a0and then to explore the prospect of using these coordinates to add some\u00a0value with\u00a0e.g.<\/em> some chiroptical calculations.<\/span><\/div>\n
I cannot really show you a diagram at this stage, since the article is not gold open access (OA) and hence is copyright protected\u00a0as \u00a9 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. So to progress I have to get the 3D coordinates, which as data cannot be copyrighted and from these generate my own diagram. How did I go about getting this data and how\u00a0FAIR (F<\/strong><\/span>indable, A<\/strong><\/span>ccessible, I<\/strong><\/span>nteroperable, R<\/strong><\/span>eusable) did I find it?\u00a0Here I list the actions\u00a0I went through.<\/div>\n
    \n
  1. Go to the article[1]<\/a><\/span> via<\/em> its “landing page” and there I (as a human) navigated to the supporting information. Could automated software have done this I wonder if it were not familiar with the journal?<\/li>\n
  2. There I found\u00a0a PDF file and two MP4 movies. I know movies are unlikely to\u00a0contain FAIR data, so I try the former. On pages 16-17 you find the space group, cell dimensions and fractional atomic coordinates. Its not really formatted to be “I” (copying\/pasting out of PDF can be a challenge) and you have to be familiar with what is a specialised format (neither A nor really R then)\u00a0and some knowledge of\u00a0appropriate crystallographic software or procedure to convert Table S1 and S2 into\u00a0an inter-operable format such as CIF (crystallographic interchange format). <\/li>\n
  3. The main article does have the following statement:\u00a0F<\/span>urther details of the crystal structure investigation(s) may be\u00a0<\/span>obtained from the F<\/span>achinformationszentrum Karlsruhe, 76344\u00a0<\/span>Eggenstein-Leopoldshafen (Germany), on quoting the depository number CSD-430054. <\/em>Do they want you to write them a letter?<\/li>\n
  4. Well, a bit of Googling\u00a0reveals\u00a0https:\/\/www.fiz-karlsruhe.de\/en\/leistungen\/kristallographie\/kristallstrukturdepot\/order-form-request-for-deposited-data.html<\/a><\/small> as the required online link (why could that not be shortened and included in the article?)<\/li>\n
  5. This form has not quite yet caught up with modern journal practice. The form stipulates a page number is apparently mandatory, but although this article is fully published, it is too new to have one. I wrote “not assigned yet” and hoped for the best; a “clever” non-human script might always decide the data type of this response is wrong and reject the request! There is no field for the article DOI, which is really all the information that is needed. I pasted that into the “volume number” and again\u00a0crossed my fingers.<\/li>\n
  6. Two days later, whilst awaiting a response to the above, I revisited Table S1\/S2 but now armed with a sample CIF file for the space group\u00a0P 2\/c and using a text editor, inserted\u00a0into it the values found in these tables (~15 minutes). The result is shown below.‡<\/sup><\/li>\n<\/ol>\n

    \"snip\"<\/p>\n

    This double helix is not of the complementary type found in DNA but a concentric one. The inner helix of a chain of P atoms is enclosed by the outer helix (winding in the same sense, anticlockwise as shown above) of a Sn-I-Sn-I chain. Click on the diagram above to load the 3D coordinates and inspect this for yourself.<\/p>\n

    The article reporting this structure[1]<\/a><\/span> is full of fascinating insights into this new material. Time will no doubt tell whether it has exploitable properties. Meanwhile, when the CIF file arrives from my query above, I will make it available here as properly FAIR data.<\/p>\n

    \n

    ‡<\/sup>Use of Java and Jmol to display models is getting more and more fraught. Although it can still be made to work if you enter the host as a security exception, this is quite a deterrent. You can see a non-Java version of this post here<\/a>. For reasons which have not been established, the JSmol plugin which enables this mode does not work at all on the present blog.
    \n<\/p>\n

    References<\/h2>\n
    1. D. Pfister, K. Sch\u00e4fer, C. Ott, B. Gerke, R. P\u00f6ttgen, O. Janka, M. Baumgartner, A. Efimova, A. Hohmann, P. Schmidt, S. Venkatachalam, L. van W\u00fcllen, U. Sch\u00fcrmann, L. Kienle, V. Duppel, E. Parzinger, B. Miller, J. Becker, A. Holleitner, R. Weihrich, and T. Nilges, \"Inorganic Double Helices in Semiconducting SnIP\", Advanced Materials<\/i>, vol. 28, pp. 9783-9791, 2016. https:\/\/doi.org\/10.1002\/adma.201603135<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      After sixty years of searching, the first non-templated double helical carbon-free inorganic molecular structure has been reported. That is so neat that I thought to load the 3D coordinates here for you to interact with\u00a0and then to explore the prospect of using these coordinates to add some\u00a0value with\u00a0e.g. some chiroptical calculations. I cannot really show […]<\/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":true,"_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":[],"ppma_author":[2661],"class_list":["post-16997","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining"],"yoast_head":"\nAn inorganic double helix: SnIP. - 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=16997\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"An inorganic double helix: SnIP. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"After sixty years of searching, the first non-templated double helical carbon-free inorganic molecular structure has been reported. 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Other journals (e.g.\u00a0Nature Chemistry ran the article as a research highlight (where the purpose\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\/2010\/11\/cbd.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":22231,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22231","url_meta":{"origin":16997,"position":2},"title":"A molecular sponge for hydrogen storage- the future for road transport?","author":"Henry Rzepa","date":"April 19, 2020","format":false,"excerpt":"In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus \"NU-1501-Al\" can absorb 14 weight% of hydrogen. 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I have already written about\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":7068,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7068","url_meta":{"origin":16997,"position":5},"title":"More joining up of pieces. Stereocontrol in the ring opening of cyclopropenes.","author":"Henry Rzepa","date":"July 12, 2012","format":false,"excerpt":"Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and\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":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/07\/dichlorocarbene.svg","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\/16997","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=16997"}],"version-history":[{"count":32,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16997\/revisions"}],"predecessor-version":[{"id":17036,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16997\/revisions\/17036"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16997"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16997"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16997"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16997"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}