{"id":16497,"date":"2016-06-10T08:26:13","date_gmt":"2016-06-10T07:26:13","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16497"},"modified":"2016-06-26T08:20:43","modified_gmt":"2016-06-26T07:20:43","slug":"a-wider-look-at-chlorine-trifluoride-crystal-structures-and-data-mining","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497","title":{"rendered":"A wider look at chlorine trifluoride: crystal structures and data mining."},"content":{"rendered":"
\n

\n\tA while ago, I explored<\/a> how the 3-coordinate halogen compound ClF3<\/sub> is conventionally analyzed using VSEPR (valence shell electron pair repulsion theory). Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the crystal structure database (CSD).\n<\/p>\n

\n\t\"\"\n<\/p>\n

\n\tThe search query specifies 7A as the central atom, defined with just three bonded (non-metallic) atoms. Initially, if no constraint on any cyclicity in the three 7A-NM bonds is made (and with R < 0.1, no errors, no disorder), the following result emerges.\n<\/p>\n

\n\t\"\"\n<\/p>\n

\n\tI have plotted the three angle variables using the X\/Y axes above and used colour to indicate the third angle (red = ~180°, blue = ~90°). The clusters show that two of the angles are ~90° and only one is ~180°. There is also a set of blue points (~90°) which show a linear correlation and which can be shown to derive from cyclicity, as the plot below reveals when acyclicity is specified for all three NM-7A bonds.\n<\/p>\n

\n\t\"\"\n<\/p>\n

\n\tIn this distribution, the two clusters for ANG1 or ANG2 of ~180° are small and compact, but the cluster where both ANG1 and ANG2 are ~90° is much more diffuse. Not all of the points in this cluster show as red (ANG3 ~180°); there are a few cyan or blue examples here too; indicating all three angles are in the range 140-90°. This result is not arising from cyclic constraints. \n<\/p>\n

\n\tThis wider look at 3-coordinate compounds in group 17 (the halogens) quickly reveals a class of such molecules where all three angles are relatively small. This suggests that a closer look at the bonding in these systems, especially in terms of VSEPR, might be rewarding!\n<\/p>\n

\n\tI end with an equivalent search for group 18 (the noble gases). Although the number of examples is small, all show the two small\/one large angle so characteristic of chlorine trifluoride itself. \n<\/p>\n

\n\t\"\"\n<\/p>\n

\n\tThe above is I think a good example of (big?) data mining, where one is searching for patterns, and if lucky spotting patterns that deviate from the norm to investigate the possibility of new chemical phenomena.[1]<\/a><\/span> It is also interesting to speculate upon the origins of why two of the clusters shown above are small and compact and the third is much more diffuse.<\/p>\n

References<\/h2>\n
  1. H.S. Rzepa, \"Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases\", Journal of Chemical Education<\/i>, vol. 93, pp. 550-554, 2015. https:\/\/doi.org\/10.1021\/acs.jchemed.5b00346<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    A while ago, I explored how the 3-coordinate halogen compound ClF3 is conventionally analyzed using VSEPR (valence shell electron pair repulsion theory). Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the crystal structure database (CSD). The search query specifies 7A as the central atom, defined with just three bonded (non-metallic) atoms. Initially, […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_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},"jetpack_post_was_ever_published":false},"categories":[1745],"tags":[1548,1091,1767,1437,1766],"ppma_author":[2661],"class_list":["post-16497","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-chemical-phenomena","tag-data-mining","tag-equivalent-search","tag-halogen","tag-search-query-specifies-7a"],"yoast_head":"\nA wider look at chlorine trifluoride: crystal structures and data mining. - 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=16497\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A wider look at chlorine trifluoride: crystal structures and data mining. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"A while ago, I explored how the 3-coordinate halogen compound ClF3 is conventionally analyzed using VSEPR (valence shell electron pair repulsion theory). Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the crystal structure database (CSD). The search query specifies 7A as the central atom, defined with just three bonded (non-metallic) atoms. Initially, […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-06-10T07:26:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-06-26T07:20:43+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/7-SQ.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":"A wider look at chlorine trifluoride: crystal structures and data mining. - 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=16497","og_locale":"en_GB","og_type":"article","og_title":"A wider look at chlorine trifluoride: crystal structures and data mining. - Henry Rzepa's Blog","og_description":"A while ago, I explored how the 3-coordinate halogen compound ClF3 is conventionally analyzed using VSEPR (valence shell electron pair repulsion theory). Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the crystal structure database (CSD). The search query specifies 7A as the central atom, defined with just three bonded (non-metallic) atoms. Initially, […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497","og_site_name":"Henry Rzepa's Blog","article_published_time":"2016-06-10T07:26:13+00:00","article_modified_time":"2016-06-26T07:20:43+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/7-SQ.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"A wider look at chlorine trifluoride: crystal structures and data mining.","datePublished":"2016-06-10T07:26:13+00:00","dateModified":"2016-06-26T07:20:43+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497"},"wordCount":403,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/7-SQ.jpg","keywords":["chemical phenomena","data mining","equivalent search","Halogen","search query specifies 7A"],"articleSection":["crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497","name":"A wider look at chlorine trifluoride: crystal structures and data mining. - Henry Rzepa's Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/7-SQ.jpg","datePublished":"2016-06-10T07:26:13+00:00","dateModified":"2016-06-26T07:20:43+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#primaryimage","url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/7-SQ.jpg","contentUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/7-SQ.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16497#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"A wider look at chlorine trifluoride: crystal structures and data mining."}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa's Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-4i5","jetpack-related-posts":[{"id":13083,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13083","url_meta":{"origin":16497,"position":0},"title":"Halogen bonds: Part 1.","author":"Henry Rzepa","date":"November 29, 2014","format":false,"excerpt":"Halogen bonds are less familiar cousins to hydrogen bonds. They are defined as non-covalent interactions (NCI) between a halogen atom (X, acting as a Lewis acid, in accepting electrons) and a Lewis base D donating electrons; D....X-A vs D...H-A. They are superficially surprising, since both D and X look like\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":"halogen-search","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/halogen-search.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":13158,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158","url_meta":{"origin":16497,"position":1},"title":"Halogen bonds 4: The strongest (?) halogen bond.","author":"Henry Rzepa","date":"December 7, 2014","format":false,"excerpt":"Continuing my hunt, here is a candidate for a strong(est?) halogen bond, this time between Se and I.. The features of interest include: The six-membered ring is in the chair conformation. The (relatively enormous) I...I substituent is axial! It is attached to the Se rather than the O. The Se...I\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":25550,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25550","url_meta":{"origin":16497,"position":2},"title":"What is the largest angle possible at 4-coordinate carbon – 180\u00b0?","author":"Henry Rzepa","date":"September 11, 2022","format":false,"excerpt":"Four-coordinate carbon normally adopts a tetrahedral shape, where the four angles at the carbon are all 109.47\u00b0. But how large can that angle get, and can it even get to be 180\u00b0? A search of the CSD (crystal structure database) reveals a spiropentane as having the largest such angle, VAJHAP\u2026","rel":"","context":"In \"Interesting chemistry\"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=interesting-chemistry"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/09\/VAJHAP-mo20-1024x758.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":17543,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17543","url_meta":{"origin":16497,"position":3},"title":"Stable “unstable” molecules: a crystallographic survey of cyclobutadienes and cyclo-octatetraenes.","author":"Henry Rzepa","date":"March 5, 2017","format":false,"excerpt":"Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965. Given that instability, I was intrigued as to how many crystal structures might have been reported for this ring system, along with the rather more\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/134-1024x722.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24483,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24483","url_meta":{"origin":16497,"position":4},"title":"Protein-Biotin complexes. Crystal structure mining.","author":"Henry Rzepa","date":"December 12, 2021","format":false,"excerpt":"In the previous post, I showed some of the diverse \"non-classical\"interactions between Biotin and a protein where it binds very strongly. Here I take a look at two of these interactions to discover how common they are in small molecule structures. The first search is of a CH hydrogen bond\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/12\/Screenshot-983-1024x893.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":16573,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16573","url_meta":{"origin":16497,"position":5},"title":"How does an OH or NH group approach an aromatic ring to hydrogen bond with its \u03c0-face?","author":"Henry Rzepa","date":"June 22, 2016","format":false,"excerpt":"I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here\u00a0I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and\u00a0OH or NH groups. I start by defining a benzene ring with a centroid.\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":"aromatic-pi-query","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/aromatic-pi-query-1-e1466580253270.jpg?resize=350%2C200","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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16497","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=16497"}],"version-history":[{"count":14,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16497\/revisions"}],"predecessor-version":[{"id":16517,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16497\/revisions\/16517"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16497"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16497"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16497"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16497"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}