{"id":13083,"date":"2014-11-29T09:48:45","date_gmt":"2014-11-29T09:48:45","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13083"},"modified":"2016-06-18T07:53:09","modified_gmt":"2016-06-18T06:53:09","slug":"halogen-bonds-part-1","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13083","title":{"rendered":"Halogen bonds: Part 1."},"content":{"rendered":"
\n

\n\tHalogen bonds are less familiar cousins to hydrogen bonds. They are defined as non-covalent interactions<\/em> (NCI) between a halogen atom (X<\/strong>, acting as a Lewis acid, in accepting electrons) and a Lewis base D<\/strong> donating electrons; D….X-A<\/strong> vs<\/em> D…H-A<\/strong>. They are superficially surprising, since both D and X look like electron rich species. In fact the electron distribution around X-X (A=X) is highly anisotropic, with the electron rich distribution (the "donor")  being in a torus encircling the bond, and an electron deficient region (the "acceptor") lying along the axis of the bond.\n<\/p>\n

\n\tI will start this simple exploration of halogen bonds by a crystal structure search, defined as below, where A<\/strong> in the above definition is also any halogen, the donor D is a tri-alkyl nitrogen donating via<\/em> a lone pair, the green contact is defined as an intermolecular distance equal to or shorter than the sum of the van der Waals radii together with an angle subtended as N…7A…7A.\n<\/p>\n

\n\t\"halogen-search\"<\/a>\n<\/p>\n

\n\tThe result of such a search is shown below:\n<\/p>\n

\n\t\"halogen-search1\"<\/a>
\n\tThere are surprises.\n<\/p>\n

    \n
  1. \n\t\tThe sparsity of hits. If the search is repeated with A<\/strong> = N, O or S, only six further hits are obtained, all with A=N <\/strong>and X=I with one example of X=Br.\n\t<\/li>\n
  2. \n\t\tThere is a hot-spot at an N…I distance of 2.37Å, a massive 1.2Å shorter than the combined van der Waals radii of N and I, and with a linear N…I-I angle.\n\t<\/li>\n<\/ol>\n

    \n\tThis next search replaces A<\/strong> with a carbon instead of a halogen. The hot-spot moves to ~2.8Å, still much shorter than the combined van der Waals radii,  and there are rather more hits this time.‡<\/sup>\n<\/p>\n

    \n\t\"N-IC\"<\/a>\n<\/p>\n

    \n\tI will next start with a simple exploration of how the electron density on I2<\/sub> changes when it accepts an electron from a donor D<\/strong> (ωB97XD\/Def2-TZVPP-PP calculation). The following is an electron density difference<\/a> isosurface (0.002au) showing how the density changes. The red phase is increased<\/em> density, which adds exo<\/em> to the bond, and the blue is decreased<\/em> density, mostly at the iodine atom but also in the centre of the bond. These changes have axial symmetry along the axis of the I-I bond.\n<\/p>\n

    \n\t\"halogen-search1\"\n<\/p>\n

    \n\tAs usual, if you want to view a 3D model of this surface, click on the graphic above.\n<\/p>\n

    \n\tThis next difference map shows the inverse, i.e.<\/em> what happens when an electron is removed from I2<\/sub> to form a radical cation. Again blue shows decreased density, and this is not axially symmetric, coming from the π-system (more specifically just one of the π-MOs;  the orthogonal π-manifold actually gains red density). This is a nice way of showing that  I2<\/sub>  accepts electrons into the σ-manifold and looses them from the π-manifold. In other words, the density responds in a very anisotropic way to addition or loss of electrons.†<\/sup>\n<\/p>\n

    \n\t\"halogen-search1\"\n<\/p>\n

    \n\tIn part 2, I will focus on one of the examples, HEKZOO[1]<\/a><\/span> as published in 2012[2]<\/a><\/span>. This is a complex between the base DABCO and molecular iodine, in which the DABCO donates electrons into that I2<\/sub> σ-manifold.\n<\/p>\n

    \n

    \n\t‡<\/sup>There are only three significant hits with D=di-alkyloxygen rather than nitrogen. The first two[3]<\/a><\/span>,[4]<\/a><\/span> involve X-A=I-I with a D…X distance of 2.8Aring; and the third X-A=Cl-Cl.\n<\/p>\n

    \n

    \n\t†<\/sup>I have now added also the density difference map for the base DABCO as a model for the donor D. Note that for this base, when an electron is lost to form the radical cation, the density reduces not just at the nitrogen lone pairs, but also the adjacent C-C bonds.\n<\/p>\n

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

    \n

    \n\tThis post is the first I have written since hearing the very sad news about the death of Paul Schleyer. He was a frequent commentator on these posts, and his towering presence over the last sixty years in chemistry will be sorely missed.\n<\/p>\n

    \n
    \n\t \n<\/div>\n

    References<\/h2>\n
    1. Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., \"CCDC 879935: Experimental Crystal Structure Determination\", 2013. https:\/\/doi.org\/10.5517\/ccyjn03<\/a>\n\n<\/li>\n
    2. A. Peuronen, A. Valkonen, M. Kortelainen, K. Rissanen, and M. Lahtinen, \"Halogen Bonding-Based \u201cCatch and Release\u201d: Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts\", Crystal Growth & Design<\/i>, vol. 12, pp. 4157-4169, 2012. https:\/\/doi.org\/10.1021\/cg300669t<\/a>\n\n<\/li>\n
    3. H. Bock, and S. Holl, \"CCDC 147854: Experimental Crystal Structure Determination\", 2001. https:\/\/doi.org\/10.5517\/cc4yvhd<\/a>\n\n<\/li>\n
    4. Walbaum, C.., Pantenburg, I.., and Meyer, G.., \"CCDC 837899: Experimental Crystal Structure Determination\", 2012. https:\/\/doi.org\/10.5517\/ccx3x0x<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      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 electron rich species. In fact […]<\/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_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":[1745,4,1086],"tags":[1296,1295,1294,1133],"ppma_author":[2661],"class_list":["post-13083","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry","category-reaction-mechanism-2","tag-crystal-structure-search","tag-d-note","tag-frequent-commentator","tag-paul-schleyer"],"yoast_head":"\nHalogen bonds: Part 1. - 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=13083\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Halogen bonds: Part 1. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 electron rich species. 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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 electron rich species. 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Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the\u00a0crystal structure database (CSD). The search query specifies\u00a07A as the central atom, defined with just\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":13105,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105","url_meta":{"origin":13083,"position":2},"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":18993,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18993","url_meta":{"origin":13083,"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":1722,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1722","url_meta":{"origin":13083,"position":4},"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":[]},{"id":18975,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18975","url_meta":{"origin":13083,"position":5},"title":"Hypervalence revisited. The odd case of hexamethyl selenium.","author":"Henry Rzepa","date":"November 7, 2017","format":false,"excerpt":"One thread that runs through this blog is that of hypervalency. It was therefore nice to come across a recent review of the concept which revisits the topic, and where a helpful summary is given of the evolving meanings over time of the term hypervalent. The key phrase \"it soon\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\/2017\/11\/165-1024x1008.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\/13083","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=13083"}],"version-history":[{"count":19,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/13083\/revisions"}],"predecessor-version":[{"id":16547,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/13083\/revisions\/16547"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=13083"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=13083"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=13083"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=13083"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}