{"id":83,"date":"2009-04-03T13:18:13","date_gmt":"2009-04-03T12:18:13","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=83"},"modified":"2013-07-19T17:21:20","modified_gmt":"2013-07-19T16:21:20","slug":"on-the-importance-of-digital-repositories-in-chemistry","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=83","title":{"rendered":"On the importance of  Digital repositories in Chemistry"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"83\">\n<p>The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it yourself. Even after 15 years of the \u00a0(chemical) Web, this can be distressingly difficult to achieve (or can it be that it is only myself who wishes to view molecules in their \u00a0<i>native<\/i> mode?). \u00a0Thus the standard mechanism is to seek out on journal pages that disarming little entry entitled \u00a0<b>supporting information<\/b> and to hope that you might find something useful embedded there. \u00a0Embedded is the correct description, since the information is often found within the confines of an Acrobat file, and has to be extracted from there. \u00a0Indeed, that is what \u00a0I had to resort to in order to write one of the blog entries below. I ground my teeth whilst doing so.\u00a0<br \/> <img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-93\" title=\"blog11\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('yellow');jmolApplet([450,450],'load wp-content\/uploads\/2009\/04\/42-557.xyz; frame 1; zoom 100;vectors  on;vectors 4;vectors scale 5.0; color vectors orange;vibration 6;connect (atomno=2) (atomno=1) partial;connect (atomno=6) (atomno=1) aromatic;connect (atomno=3) (atomno=2) aromatic;connect (atomno=5) (atomno=4) aromatic;connect (atomno=3) (atomno=4) aromatic;connect (atomno=6) (atomno=5) partial;');\" alt=\"blog11\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/blog11.jpg\" width=\"304\" height=\"287\" \/><br \/> So is there a better way? We think so! The \u00a0<strong>digital repository<\/strong>. If you click on <a href=\"http:\/\/hdl.handle.net\/10042\/to-2117\" target=\"new\">this<\/a> you should see the entry directly. What can you do there? Well, if you have suitable programs, you can download eg a <em>Checkpoint<\/em> file of the calculation that created the molecule model and re-activate it there. Or you can download just the <strong>CML<\/strong> file for viewing in any CML-compliant program (such as e.g. Jmol). Or you can check up on the <b>InCHi<\/b> string or the <b>InChI Key<\/b> of the molecule.<\/p>\n<p>What about the specific entry above? Well, it corresponds to the calculation for the \u03c04 + \u03c02 cycloaddition described in the blog entry below. You can now verify for yourself the assertions made in that entry, ie that the rotation mode is disrotatory, or that the bond is forming antarafacially. You do not need to take my word for it! If the Digital repository is too much trouble for you, click on the graphic instead to get a similar result.<\/p>\n<p>We now regularly put such links into journal articles, in the form of <em>Web-enhanced<\/em> tables and figures, so that it is literally just one click away from such an article to having a vibrant molecule dancing in front of you. All (chemistry) journals should do this. If they do not yet, then contact their editor in chief when you next submit an article and ask them why not!<\/p>\n<p>See also the blog by <a href=\"http:\/\/wwmm.ch.cam.ac.uk\/blogs\/murrayrust\/\" rel=\"friend colleague\">Peter Murray-Rust.<\/a><\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 83 -->","protected":false},"excerpt":{"rendered":"<p>The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it [&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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2],"tags":[29,904,27,26,2647,30,1108,31,28],"ppma_author":[2661],"class_list":["post-83","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-acrobat","tag-checkpoint","tag-chemical","tag-chemical-behaviour","tag-chemical-it","tag-editor-in-chief","tag-opendata","tag-peter-murray-rust","tag-web-enhanced-tables"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>On the importance of Digital repositories in Chemistry - 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=83\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"On the importance of Digital repositories in Chemistry - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=83\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2009-04-03T12:18:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-07-19T16:21:20+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/blog11.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":"On the importance of Digital repositories in Chemistry - 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=83","og_locale":"en_GB","og_type":"article","og_title":"On the importance of Digital repositories in Chemistry - Henry Rzepa&#039;s Blog","og_description":"The preceeding blog entries contain stories about chemical behaviour. 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