{"id":18385,"date":"2017-05-29T17:36:22","date_gmt":"2017-05-29T16:36:22","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18385"},"modified":"2017-05-30T07:36:03","modified_gmt":"2017-05-30T06:36:03","slug":"challenges-in-reliably-representing-the-chemistry-of-crystal-structures","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18385","title":{"rendered":"Challenges in reliably representing the chemistry of crystal structures."},"content":{"rendered":"
\n

The title here is taken from a presentation made by Ian Bruno from CCDC at the recent conference on Open Science<\/a>. It also addresses the theme here<\/a>\u00a0of the issues that might arise in assigning identifiers for any given molecule.<\/p>\n

The structure was represented as shown[1]<\/a><\/span> by the original authors, in which the bonding from S to Sn is indicated with both solid lines (a bond) and dotted lines\u00a0(an “interaction”).\"\"<\/p>\n

Why would this matter? Well, to\u00a0enable any entry in the Cambridge structure database as\u00a0findable (the F of FAIR) it has to be given a unique identifier. There are in general three such identifiers assigned by the CCDC:<\/p>\n

    \n
  1. The Refcode<\/strong>, in this case XONHIS. These six or seven letter codes are historically the oldest, and started off at least with an attempt if possible to assign some semantic inference from the name, even if only occasionally.\u00a0<\/li>\n
  2. The CCDC deposition number<\/strong>, in this case 650011. This is the number that an author will receive immediately upon deposition, and you often find these identifiers quoted in supporting information files<\/li>\n
  3. The DOI<\/strong> (digital object identifier), in this case\u00a010.5517\/ccptd3z<\/a>, which can be used to view the structure even if access to the full CSD is not available to the user. In that sense, the DOI is the FAIRest of the first three of these identifiers.<\/li>\n
  4. However, CCDC reported that they are considering adding a 4th very common identifier, based on the InChI<\/strong> (International chemical identifier), which comes as a full string and with the structure of the molecule at least in part inferrable from it, together with \u00a0a shortened (almost) unique string which has the advantage of being “Googlable”. Both are\u00a0helpfully FAIR.<\/li>\n<\/ol>\n

    It is this 4th identifier that is at issue here. InChIs are derived from atom connection tables; you need to define all bonds present in the molecule. And it is here that the dotted “bond”\/”interaction” above becomes a problem. This is the representation shown in the CSD database, which reveals that all the Sn…S interactions are classified as “bonds”, along with some creative(!) representations of the C…S bonds.\"\"<\/p>\n

    So the InChI will very much depend on whether all the Sn…S contacts are termed as bonds or as interactions. To help clarify that, it is useful to show the typical range of lengths of such contacts. Below is a simple search for all Sn and S systems where the pair are either close in space (< 3.5\u00c5) or have a bond specified between the two atoms.<\/p>\n

    \"\"<\/p>\n

    The main cluster occurs at ~2.5\u00c5, but there is some evidence of a second peak at about 3.0\u00c5. The third distribution up to 3.5\u00c5 is probably a continuum of very weak dispersion interaction, which most molecules exhibit. The values for XONHIS are 2.521 and 2.996\u00c5, which match the two clusters above.<\/p>\n

    So perhaps a quantum calculation can shed some light (DOI:\u00a010.14469\/hpc\/2593<\/a>)? The values on the right are the optimised bond lengths which are pretty similar to the crystal structure. On the left are the calculated Wiberg bond orders (B3LYP+D3BJ\/Def2-TZVPP\/chloroform calculation). These reveal both “bonds” have an order less than 1. The value of ~0.6 is probably not contentious, but it does graphically show that when a compound is indexed as having a “single bond” between two atoms, the quantitative bond order may be substantially less. What however would one make of a bond order of 0.214? Should it be classified as a bond, albeit a much weaker one than normal? Or should it instead simply be a rather strong “interaction” which is not classified as a bond? And perhaps one should have in mind the question “how sensitive is this result to the quantum mechanical procedure used?”\"\"<\/p>\n

    Why does this distinction matter? Well, the InChI algorithm is based on simple connectivity; are two atoms connected by a bond or not? There are no nuances here. At the moment, this decision can be made by an algorithm based on the distance between any atom pair (whether computed or measured), but more often I suspect it derives from a “molfile” which is often derived from a human-drawn representation using a structure drawing program. It does rather boil down to the individual preferences of the human drawing the molecule. Due in part to such uncertainties, it was\u00a0estimated that only 22% of structures in the CSD can be used to generate a reliable InChI. Hydrogen bonds are almost always classified as non-bonds, which means their presence is rarely systematically flagged during the indexing of the structures. Organometallics often pose some of the greatest representational\u00a0problems\u00a0(there are many others).<\/p>\n

    I will end by observing another class of structure that I deal with, “reaction transition states”. As you might imagine these forms are full of pairs of atoms with ambiguous bond lengths and hence connectivity. We currently have no truly reliable\u00a0method for assigning useful identifiers to them. So lots of challenges for the future then!<\/p>\n

     <\/p>\n

    References<\/h2>\n
    1. R. Reyes-Mart\u00ednez, R. Mejia-Huicochea, J.A. Guerrero-Alvarez, H. H\u00f6pfl, and H. Tlahuext, \"Synthesis, heteronuclear NMR and X-ray crystallographic studies of two dinuclear diorganotin(IV) dithiocarbamate macrocycles\", Arkivoc<\/i>, vol. 2008, pp. 19-30, 2007. https:\/\/doi.org\/10.3998\/ark.5550190.0009.503<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      The title here is taken from a presentation made by Ian Bruno from CCDC at the recent conference on Open Science. It also addresses the theme here\u00a0of the issues that might arise in assigning identifiers for any given molecule. The structure was represented as shown by the original authors, in which the bonding from S […]<\/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":[281,2181,2183,806,2167,2180,2182],"ppma_author":[2661],"class_list":["post-18385","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-author","tag-bruno","tag-chemical-identifier","tag-digital-object-identifier","tag-ian-bruno","tag-identifier","tag-inchi-algorithm"],"yoast_head":"\nChallenges in reliably representing the chemistry of crystal structures. - 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=18385\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Challenges in reliably representing the chemistry of crystal structures. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The title here is taken from a presentation made by Ian Bruno from CCDC at the recent conference on Open Science. 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Here I test that F using the DataCite search service. Firstly an introduction to this service. This is a metadata database about datasets and other research objects. One of the properties is\u00a0relatedIdentifier which records other identifiers\u2026","rel":"","context":"In "Chemical IT"","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":12932,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12932","url_meta":{"origin":18385,"position":2},"title":"One molecule, one identifier: Viewing molecular files from a digital repository using metadata standards.","author":"Henry Rzepa","date":"September 8, 2014","format":false,"excerpt":"In the beginning (taken here as\u00a0prior to ~1980) libraries held\u00a0five-year printed consolidated indices of molecules, organised by formula or name (Chemical abstracts). This could occupy about 2m of shelf space for each five years. And an equivalent set of printed volumes from the Beilstein collection. Those of us who needed\u2026","rel":"","context":"In "Chemical IT"","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":24723,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24723","url_meta":{"origin":18385,"position":3},"title":"Raw data: the evolution of FAIR data and crystallography.","author":"Henry Rzepa","date":"March 1, 2022","format":false,"excerpt":"Scientific data in chemistry has come a long way in the last few decades. Originally entangled into scientific articles in the form of tables of numbers or diagrams, it was (partially) disentangled into supporting information when journals became electronic in the late 1990s. The next phase was the introduction of\u2026","rel":"","context":"In "Chemical IT"","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":17237,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17237","url_meta":{"origin":18385,"position":4},"title":"Molecules of the year? Pnictogen chains and 16 coordinate Cs.","author":"Henry Rzepa","date":"December 19, 2016","format":false,"excerpt":"I am completing my survey of the vote for molecule of the year candidates, which this year seems focused on chemical records of one type or another. The first article reports striving towards creating a molecule covering a complete column of the period table. In this case, group 7, containing\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":16251,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16251","url_meta":{"origin":18385,"position":5},"title":"Metametadata: data about data about (chemical) data.","author":"Henry Rzepa","date":"April 16, 2016","format":false,"excerpt":"Scientists are familiar with the term data, at least in a scientific or chemical context, but appreciating metadata (meaning \"after\", or \"beyond\") is slightly more subtle, in the sense of using it to mean data about data. The challenge lies in clarifying where the boundary between data and its metadata\u2026","rel":"","context":"In "Chemical IT"","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":[]}],"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\/18385","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=18385"}],"version-history":[{"count":8,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18385\/revisions"}],"predecessor-version":[{"id":18398,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18385\/revisions\/18398"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18385"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18385"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18385"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18385"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}