{"id":10825,"date":"2013-07-05T10:06:19","date_gmt":"2013-07-05T09:06:19","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10825"},"modified":"2013-07-19T17:10:26","modified_gmt":"2013-07-19T16:10:26","slug":"150000000-dft-calculations-on-2300000-compounds","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10825","title":{"rendered":"150,000,000 DFT calculations on 2,300,000 compounds!"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"10825\">\n<p>The title of this post summarises the contents of a new molecular database:\u00a0<a href=\"http:\/\/www.molecularspace.org\/\" target=\"_blank\">www.molecularspace.org<\/a><span id=\"cite_ITEM-10825-0\" name=\"citation\"><a href=\"#ITEM-10825-0\">[1]<\/a><\/span> and I picked up on it by following <a href=\"http:\/\/www.compchemhighlights.org\/2013\/06\/molecularspaceorg.html\" target=\"_blank\">the post by Jan Jensen<\/a> at\u00a0<a href=\"http:\/\/www.compchemhighlights.org\" target=\"_blank\">www.compchemhighlights.org<\/a> (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called &#8220;<em>The Harvard Clean Energy Project: Large-scale computational screening and design of organic photovoltaics on the world community grid<\/em>&#8220;. It reminds of a 2005 project by Peter Murray-Rust <em>et al<\/em> at the same sort of concept<span id=\"cite_ITEM-10825-1\" name=\"citation\"><a href=\"#ITEM-10825-1\">[2]<\/a><\/span> (the World-Wide-Molecular-Matrix, or <strong>WWMM<\/strong><span id=\"cite_ITEM-10825-2\" name=\"citation\"><a href=\"#ITEM-10825-2\">[3]<\/a><\/span>), although the new scale is certainly impressive. Here I report my initial experiences looking through molecularspace.org<\/p>\n<p>The 150,000,000 calculations are released under the the CC-BY license, which is an encouraging (open) start. One does need however to login to the site, which I was able to do using my Google credentials. Shown below is a screenshot of a typical result in a search (of Power conversion efficiency in my case).<\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"aligncenter wp-image-10827\" alt=\"CEPDB1\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/CEPDB1.jpeg\" width=\"480\" \/><\/p>\n<p>It comes in two parts, the first being the structure (given as a SMILES and 2D layout) with the principle predicted energy levels and predicted photovoltaic performance listed below that. This is then followed by what might be called an annotation with further computed\/predicted properties using the algorithms applied by Chemicalize.org. This idea that a data set could accrete via semantically powerful annotations using other tools was also very much part of the concept of the WWMM (the matrix had at its heart a molecule in one dimension and a property, measured or computed in the other. The matrix is of course very sparse, which is why it needs annotation!).<\/p>\n<p>It was at this point however that I started to wonder how I might add other annotations, based perhaps on other types of calculations. But thus far at least, I have not found any trace of something which I could immediately use for my own calculation; 3D coordinates specifically. Thus, the HOMO-LUMO energy gap is the key property which makes <strong>molecularspace<\/strong> unique and valuable (to someone working in the field of photovoltaics). But HOMO\/LUMO gaps can be calculated in many different ways, and it can always be valuable to calibrate\/validate the reported values against other methods. Perhaps if I continue to look, I might find these 3D coordinates (which, for 2,300,000 molecules would be a very valuable resource). \u00a0Certainly for example, should \u00a0I wish to do so, I could not at the moment readily replicate the calculation for any specific entry on the\u00a0<strong>molecularspace <\/strong>site (which can be regarded as an essential component of scientific validation). When I use the first person, I mean of course either myself as a human or a software agent acting on my behalf (the latter having the endurance to repeat its procedures millions of times if necessary).\u00a0<\/p>\n<p>The reader of this blog may have noticed that whenever I report a calculation here, I like to cite its doi (more formally its <strong>handle<\/strong>), which links to a digital repository. In my case, the repository certainly carries the 3D coordinates, and also the full wavefunction provided if the reader wishes other properties to be derived from it.<sup>\u2021<\/sup> Now if\u00a0<strong>molecularspace <\/strong>is able to provide that in the fullness of time, it truly would be an impressive resource.<\/p>\n<p>But the important take-home message from\u00a0<strong>molecularspace<\/strong> is that archiving (under a\u00a0CC-BY license) the &#8220;big&#8221; data from any given research in a manner which makes it readily re-usable by others (perhaps from quite different fields of science) is now an essential requisite of doing science. And it is really nice to see good examples of this in practice!<\/p>\n<hr \/>\n<p><sup>\u2021<\/sup> Generally, the calculations I perform for this blog are published in a DSpace repository (the <a href=\"https:\/\/spectradspace.lib.imperial.ac.uk:8443\/dspace\/handle\/10042\/13\" target=\"_blank\">original one,<\/a> started in 2006<span id=\"cite_ITEM-10825-3\" name=\"citation\"><a href=\"#ITEM-10825-3\">[4]<\/a><\/span>), and more recently in <a href=\"http:\/\/chempound.ch.ic.ac.uk:8090\" target=\"_blank\">Chempound<\/a> (a<a href=\"http:\/\/journals.tdl.org\/jodi\/index.php\/jodi\/article\/view\/5873\/5879\" target=\"_blank\"> project by Peter Murray-Rust and colleagues<\/a> which emerged out of the WWMM experiments) as well as Figshare<span id=\"cite_ITEM-10825-4\" name=\"citation\"><a href=\"#ITEM-10825-4\">[5]<\/a><\/span>. The first and the third assign <a title=\"Research data and the \u201ch-index\u201d.\" href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10736\" target=\"_blank\">unique handles<\/a> (<em>i.e.<\/em> a <strong>doi<\/strong>) to the data; chempound does not (and neither does molecularspace).<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-10825-0\">J. Hachmann, R. Olivares-Amaya, S. Atahan-Evrenk, C. Amador-Bedolla, R.S. S\u00e1nchez-Carrera, A. Gold-Parker, L. Vogt, A.M. Brockway, and A. Aspuru-Guzik, \"The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid\", <i>The Journal of Physical Chemistry Letters<\/i>, vol. 2, pp. 2241-2251, 2011. <a href=\"https:\/\/doi.org\/10.1021\/jz200866s\">https:\/\/doi.org\/10.1021\/jz200866s<\/a>\n\n<\/li>\n<li id=\"ITEM-10825-1\">P. Murray-Rust, H.S. Rzepa, J.J.P. Stewart, and Y. Zhang, \"A global resource for computational chemistry\", <i>Journal of Molecular Modeling<\/i>, vol. 11, pp. 532-541, 2005. <a href=\"https:\/\/doi.org\/10.1007\/s00894-005-0278-1\">https:\/\/doi.org\/10.1007\/s00894-005-0278-1<\/a>\n\n<\/li>\n<li id=\"ITEM-10825-2\">P. Murray-Rust, S.E. Adams, J. Downing, J.A. Townsend, and Y. Zhang, \"The semantic architecture of the World-Wide Molecular Matrix (WWMM)\", <i>Journal of Cheminformatics<\/i>, vol. 3, 2011. <a href=\"https:\/\/doi.org\/10.1186\/1758-2946-3-42\">https:\/\/doi.org\/10.1186\/1758-2946-3-42<\/a>\n\n<\/li>\n<li id=\"ITEM-10825-3\">J. Downing, P. Murray-Rust, A.P. Tonge, P. Morgan, H.S. Rzepa, F. Cotterill, N. Day, and M.J. Harvey, \"SPECTRa: The Deposition and Validation of Primary Chemistry Research Data in Digital Repositories\", <i>Journal of Chemical Information and Modeling<\/i>, vol. 48, pp. 1571-1581, 2008. <a href=\"https:\/\/doi.org\/10.1021\/ci7004737\">https:\/\/doi.org\/10.1021\/ci7004737<\/a>\n\n<\/li>\n<li id=\"ITEM-10825-4\">H.S. Rzepa, \"Gaussian Job Archive for CLi6\", 2013. <a href=\"https:\/\/doi.org\/10.6084\/m9.figshare.739310\">https:\/\/doi.org\/10.6084\/m9.figshare.739310<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 10825 -->","protected":false},"excerpt":{"rendered":"<p>The title of this post summarises the contents of a new molecular database:\u00a0www.molecularspace.org and I picked up on it by following the post by Jan Jensen at\u00a0www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called &#8220;The Harvard Clean Energy Project: Large-scale computational screening and design of organic [&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":[2],"tags":[212,64,59,1100,359,1098,1108,31,1099,1101,1102],"ppma_author":[2661],"class_list":["post-10825","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-energy-gap","tag-energy-levels","tag-google","tag-harvard","tag-jan-jensen","tag-molecularspace-site","tag-opendata","tag-peter-murray-rust","tag-software-agent-acting","tag-www-compchemhighlights-org","tag-www-molecularspace-org"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>150,000,000 DFT calculations on 2,300,000 compounds! - 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=10825\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"150,000,000 DFT calculations on 2,300,000 compounds! - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The title of this post summarises the contents of a new molecular database:\u00a0www.molecularspace.org and I picked up on it by following the post by Jan Jensen at\u00a0www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called &#8220;The Harvard Clean Energy Project: Large-scale computational screening and design of organic [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10825\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-07-05T09:06:19+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-07-19T16:10:26+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/CEPDB1.jpeg\" \/>\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":"150,000,000 DFT calculations on 2,300,000 compounds! - 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=10825","og_locale":"en_GB","og_type":"article","og_title":"150,000,000 DFT calculations on 2,300,000 compounds! - Henry Rzepa&#039;s Blog","og_description":"The title of this post summarises the contents of a new molecular database:\u00a0www.molecularspace.org and I picked up on it by following the post by Jan Jensen at\u00a0www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). 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So in this respect, 1994 is now\u2026","rel":"","context":"In &quot;Chemical IT&quot;","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":14224,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14224","url_meta":{"origin":10825,"position":1},"title":"The 2015 Bradley-Mason prize for open chemistry.","author":"Henry Rzepa","date":"June 26, 2015","format":false,"excerpt":"Open principles in the sciences in general and chemistry in particular are increasingly nowadays preached from funding councils down, but it can be more of a challenge to find innovative\u00a0practitioners. Part of the problem perhaps is that many of the current reward systems for scientists do not always help promote\u2026","rel":"","context":"In &quot;Bradley-Mason Prize for Open Chemistry&quot;","block_context":{"text":"Bradley-Mason Prize for Open Chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2131"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":28233,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28233","url_meta":{"origin":10825,"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":10990,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10990","url_meta":{"origin":10825,"position":3},"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 &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":15671,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15671","url_meta":{"origin":10825,"position":4},"title":"A molecular balance for dispersion energy?","author":"Henry Rzepa","date":"February 7, 2016","format":false,"excerpt":"The geometry of cyclo-octatetraenes differs fundamentally from the lower homologue benzene in exhibiting slow (nuclear) valence bond isomerism rather than rapid (electronic) bond-equalising resonance. In 1992 Anderson and Kirsch exploited this property to describe a simple molecular balance for\u00a0estimating how two alkyl substituents on the ring might interact via the\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":16402,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16402","url_meta":{"origin":10825,"position":5},"title":"The mechanism of silylether deprotection using a tetra-alkyl ammonium fluoride.","author":"Henry Rzepa","date":"May 25, 2016","format":false,"excerpt":"The substitution of a nucleofuge (a good leaving group) by a nucleophile at a carbon centre\u00a0occurs with inversion\u00a0of configuration at the carbon, the mechanism being known by\u00a0the term\u00a0SN2\u00a0(a story I have also told\u00a0in this post). Such displacement at silicon famously proceeds by a quite different mechanism, which\u00a0I here quantify with\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","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":[]}],"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\/10825","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=10825"}],"version-history":[{"count":16,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10825\/revisions"}],"predecessor-version":[{"id":10923,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10825\/revisions\/10923"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=10825"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=10825"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=10825"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=10825"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}