{"id":13158,"date":"2014-12-07T10:28:22","date_gmt":"2014-12-07T10:28:22","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13158"},"modified":"2016-06-18T07:52:36","modified_gmt":"2016-06-18T06:52:36","slug":"halogen-bonds-4-the-strongest-halogen-bond","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158","title":{"rendered":"Halogen bonds 4: The strongest (?) halogen bond."},"content":{"rendered":"
\n

\n\tContinuing my hunt<\/a>, here is a candidate for a strong(est?) halogen bond, this time between Se and I.[1]<\/a><\/span>. \"OXSELI\"<\/a> The features of interest include:\n<\/p>\n

    \n
  1. \n\t\tThe six-membered ring is in the chair conformation.\n\t<\/li>\n
  2. \n\t\tThe (relatively enormous) I…I substituent is axial<\/strong>!\n\t<\/li>\n
  3. \n\t\tIt is attached to the Se rather than the O.\n\t<\/li>\n
  4. \n\t\tThe Se…I distance is 2.75Å, some 1.13Å shorter than the combined atom ver der Waals radii (1.90 + 1.98 = 3.88)\n\t<\/li>\n
  5. \n\t\tThe Wiberg bond index is 0.42 for the Se-I bond and 0.63 for the I-I bond (at the crystal geometry). It is tending towards a symmetrical disposition of the central iodine (a feat also achieved<\/a> by the iodine in the NI3<\/sub> complex).\n\t<\/li>\n
  6. \n\t\tThe NBO E(2) perturbation involving donation from the Se lone pair into the I-I antibond is 77<\/strong> kcal\/mol, almost twice the value of the one involving DABCO…I-I<\/a> and way above the values found for the related hydrogen bond.\n\t<\/li>\n
  7. \n\t\tThe B3LYP+D3\/Def2-TZVPP+PP(I) optimised structure expands the Se-I bond distance to 3.04 and contracts the I-I distance to 2.81Å indicating (as with DABCO…I-I) that there may be compression of this bond induced by the lattice.\n\t<\/li>\n
  8. \n\t\tThe NCI surface shows a classical "strong" interaction between Se and I (blue), but significant additional features arising from the axial hydrogens that might account for the axial orientation of the Se…I-I group.
    \"Click

    Click for 3D<\/p><\/div>\n\t<\/li>\n

  9. \n\t\tFor good measure, here is the complete crystal structure search, defining any non-bonded contact between any element of group six and group seven that is <0.5Å shorter than the van del Waals contact. Our candidate is on the left hand edge of the plot. \"Se-I\"<\/a>\n\t<\/li>\n<\/ol>\n

    References<\/h2>\n
    1. H. Maddox, and J.D. McCullough, \"The Crystal and Molecular Structure of the Iodine Complex of 1-Oxa-4-selenacyclohexane, C<sub>4<\/sub>H<sub>8<\/sub>OSe.I<sub>2<\/sub>\", Inorganic Chemistry<\/i>, vol. 5, pp. 522-526, 1966. https:\/\/doi.org\/10.1021\/ic50038a006<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      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 distance is 2.75Å, some 1.13Å […]<\/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":[1745,4],"tags":[48,1296],"ppma_author":[2661],"class_list":["post-13158","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry","tag-chair","tag-crystal-structure-search"],"yoast_head":"\nHalogen bonds 4: The strongest (?) halogen bond. - 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=13158\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Halogen bonds 4: The strongest (?) halogen bond. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 distance is 2.75Å, some 1.13Å […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2014-12-07T10:28:22+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-06-18T06:52:36+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/12\/OXSELI.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=\"1 minute\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Halogen bonds 4: The strongest (?) halogen bond. - 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=13158","og_locale":"en_GB","og_type":"article","og_title":"Halogen bonds 4: The strongest (?) halogen bond. - Henry Rzepa's Blog","og_description":"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 distance is 2.75Å, some 1.13Å […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158","og_site_name":"Henry Rzepa's Blog","article_published_time":"2014-12-07T10:28:22+00:00","article_modified_time":"2016-06-18T06:52:36+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/12\/OXSELI.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Halogen bonds 4: The strongest (?) halogen bond.","datePublished":"2014-12-07T10:28:22+00:00","dateModified":"2016-06-18T06:52:36+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158"},"wordCount":288,"commentCount":7,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/12\/OXSELI.jpg","keywords":["chair","crystal structure search"],"articleSection":["crystal_structure_mining","Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158","name":"Halogen bonds 4: The strongest (?) halogen bond. - 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=13158#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/12\/OXSELI.jpg","datePublished":"2014-12-07T10:28:22+00:00","dateModified":"2016-06-18T06:52:36+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=13158#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158#primaryimage","url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/12\/OXSELI.jpg","contentUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/12\/OXSELI.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13158#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"Halogen bonds 4: The strongest (?) halogen bond."}]},{"@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\/pDef7-3qe","jetpack-related-posts":[{"id":13083,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13083","url_meta":{"origin":13158,"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":13105,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105","url_meta":{"origin":13158,"position":1},"title":"Halogen bonds 2: The DABCO-Iodine structure.","author":"Henry Rzepa","date":"November 30, 2014","format":false,"excerpt":"Pursuing the topic of halogen bonds, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO as published in 2012 and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as\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":"","width":0,"height":0},"classes":[]},{"id":13136,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13136","url_meta":{"origin":13158,"position":2},"title":"Halogen bonds 3: “Nitrogen tri-iodide”","author":"Henry Rzepa","date":"December 1, 2014","format":false,"excerpt":"Nitrogen tri-iodide, or more accurately the complex between it and ammonia ranks amongst the oldest known molecules (1812). I became familiar with it around the age of 12-13, in an era long gone when boys (and very possibly girls too) were allowed to make such substances in their parent's back\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":"","width":0,"height":0},"classes":[]},{"id":18993,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18993","url_meta":{"origin":13158,"position":3},"title":"VSEPR Theory: Octet-busting or not with trimethyl chlorine, ClMe3.","author":"Henry Rzepa","date":"November 12, 2017","format":false,"excerpt":"A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five \"electron\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":23588,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23588","url_meta":{"origin":13158,"position":4},"title":"Two new reality-based suggestions for molecules with a metal M\u2a78C quadruple bond.","author":"Henry Rzepa","date":"May 8, 2021","format":false,"excerpt":"Following from much discussion over the last decade about the nature of C2, a diatomic molecule which some have suggested sustains a quadruple bond between the two carbon atoms, new ideas are now appearing for molecules in which such a bond may also exist between carbon and a transition metal\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\/05\/Screenshot-702-300x63.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":1722,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1722","url_meta":{"origin":13158,"position":5},"title":"Quintuple bonds: part 2","author":"Henry Rzepa","date":"February 20, 2010","format":false,"excerpt":"In the previous post, I ruminated about how chemists set themselves targets. Thus, having settled on describing regions between two (and sometimes three) atoms as bonds, they added a property of that bond called its order. The race was then on to find molecules which exhibit the highest order between\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/02\/f2-elf1.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/02\/f2-elf1.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/02\/f2-elf1.jpg?resize=525%2C300&ssl=1 1.5x"},"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\/13158","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=13158"}],"version-history":[{"count":13,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/13158\/revisions"}],"predecessor-version":[{"id":16546,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/13158\/revisions\/16546"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=13158"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=13158"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=13158"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=13158"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}