{"id":13105,"date":"2014-11-30T16:56:13","date_gmt":"2014-11-30T16:56:13","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13105"},"modified":"2014-12-03T16:49:42","modified_gmt":"2014-12-03T16:49:42","slug":"halogen-bonds-2-the-dabco-iodine-structure","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105","title":{"rendered":"Halogen bonds 2: The DABCO-Iodine structure."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"13105\">\n<p>Pursuing the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13083\" title=\"Halogen bonds: Part 1.\" target=\"_blank\">topic of halogen bonds<\/a>, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO<span id=\"cite_ITEM-13105-0\" name=\"citation\"><a href=\"#ITEM-13105-0\">[1]<\/a><\/span> as published in 2012<span id=\"cite_ITEM-13105-1\" name=\"citation\"><a href=\"#ITEM-13105-1\">[2]<\/a><\/span> and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as a &#8220;non-covalent-interaction&#8221; (NCI) or not.<\/p>\n<p>The crystal structure shows a repeating unit, with each DABCO surrounded by two I<sub>2<\/sub> molecules aligned along the N-N axis. These linear chains are stacked in a dislocated manner induced by aligning to optimize the dispersion interactions between the iodines and the CH groups. The most surprising aspect is the N&#8230;I distance shown as 2.42&Aring;. The van der Waals radii of N and I are respectively 1.55 + 1.98 = 3.53&Aring;, a contraction of 1.1&Aring;. The covalent radii are 0.75 + 1.33 = 2.08, an elongation of 0.34&Aring; So is this a strong (non-covalent) interaction\/contraction or a stretched weak covalent bond?<\/p>\n<p>I will start with a B3LYP+D3\/Def2-TZVPP+PP calculation on the crystal geometry (below).<\/p>\n<div id=\"attachment_13106\" style=\"width: 410px\" class=\"wp-caption aligncenter\"><img decoding=\"async\" aria-describedby=\"caption-attachment-13106\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2014\/11\/HEKZOO.cif;spin 3;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.jpg\" alt=\"Click for 3D\" width=\"400\" class=\"size-full wp-image-13106\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.jpg 992w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO-300x125.jpg 300w\" sizes=\"(max-width: 992px) 100vw, 992px\" \/><p id=\"caption-attachment-13106\" class=\"wp-caption-text\">Click for 3D<\/p><\/div>\n<p>The short N&#8230;I distance has a computed Wiberg bond order of 0.26 (the I-I is 0.76) and an E(2) NBO donor-acceptor interaction energy of 40.1 kcal\/mol. For comparison, the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=8860\" title=\"Hydrogen bond strength as a function of ring size.\" target=\"_blank\"> E(2) energies for conventional OH&#8230;O hydrogen bonds<\/a> are around 10 kcal\/mol. This makes the halogen bond a pretty strong interaction! But is it strong enough to call a bond? Indeed, do we have any means of deciding where the transition from a strong interaction to a weak bond occurs?<\/p>\n<p>A NCI analysis is shown below. This analysis filters out electron densities above 0.05au (which are considered as covalent values) and shows only the properties of the reduced density gradients below this value. The dispersion attractions between the DABCO hydrocarbon chains and the iodine molecules are very apparent, but the N&#8230;I is encircled with a strange feature, normally only seen for covalent bonds or transition state breaking\/forming bonds. A strong hydrogen bond for example would show up as blue, and not this strange torus.<\/p>\n<div id=\"attachment_13116\" style=\"width: 410px\" class=\"wp-caption aligncenter\"><img decoding=\"async\" aria-describedby=\"caption-attachment-13116\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2014\/11\/HEKZOO_denl.cub.xyz;isosurface colour red blue wp-content\/uploads\/2014\/11\/HEKZOO_denl.cub.jvxl translucent;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-NCI.jpg\" alt=\"Click for 3D\" width=\"400\"  class=\"size-full wp-image-13116\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-NCI.jpg 480w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-NCI-300x150.jpg 300w\" sizes=\"(max-width: 480px) 100vw, 480px\" \/><p id=\"caption-attachment-13116\" class=\"wp-caption-text\">Click for 3D<\/p><\/div>\n<p>Reducing the threshold for covalent densities to be filtered out to 0.03au eliminates the N&#8230;I feature (it is now covalent by definition so to speak), but the I-I feature remains. One can see here that this NCI analysis does rather arbitrarily depend on what one considers the covalent density threshold to be, and as one moves up the periodic table, this density changes. What should the density for eg a N&#8230;I interaction\/bond actually be? The value appropriate for N (0.05) or I (< 0.03)?<br \/>\n<div id=\"attachment_13119\" style=\"width: 410px\" class=\"wp-caption aligncenter\"><img decoding=\"async\" aria-describedby=\"caption-attachment-13119\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2014\/11\/HEKZOO_denl1.cub.xyz;isosurface colour red blue wp-content\/uploads\/2014\/11\/HEKZOO_denl1.cub.jvxl translucent;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-NCI-0.03.jpg\" alt=\"Click for 3D\" width=\"400\" class=\"size-full wp-image-13119\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-NCI-0.03.jpg 584w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-NCI-0.03-300x127.jpg 300w\" sizes=\"(max-width: 584px) 100vw, 584px\" \/><p id=\"caption-attachment-13119\" class=\"wp-caption-text\">Click for 3D<\/p><\/div><\/p>\n<p>Next, I show the optimised geometry of the system above.<span id=\"cite_ITEM-13105-2\" name=\"citation\"><a href=\"#ITEM-13105-2\">[3]<\/a><\/span> This is not a periodic boundary calculation and this lack of a surrounding environment is highlighted by the change in the structure. The N&#8230;I distance lengthens, and the iodines which have no DABCO to interact with lengthen more. One might conclude that the short N&#8230;I distance measured in the solid state structure is due to some degree of N&#8230;I compression induced by the linear chains of I-I&#8230;DABCO&#8230;I-I&#8230;DABCO&#8230;I-I aligning to maximise the interchain dispersion attractions. Thus the N&#8230;I &#8220;<em>bond\/interaction<\/em>&#8221; is really a co-operative effect between the N&#8230;I atoms and the extended 3D structure of the molecule. The N&#8230;I contraction of 1.1&Aring; noted above is in part due to the intrinsic halogen bond, but also in part due to dispersion attractions elsewhere!<br \/>\n<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-opt.jpg\"><img decoding=\"async\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-opt.jpg\" alt=\"DAB-opt\" width=\"400\" class=\"aligncenter size-full wp-image-13124\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-opt.jpg 936w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DAB-opt-300x123.jpg 300w\" sizes=\"(max-width: 936px) 100vw, 936px\" \/><\/a><\/p>\n<p>So it does rather seem as if the DABCO-I<sub>2<\/sub> complex sits very much in that awkward region in which the contracted N&#8230;I distance could either be described as a weak bond or a strong interaction.<sup>&Dagger;<\/sup>. Just like the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=11331\" title=\"A short non-bonding H\u2026H interaction (continued)\" target=\"_blank\">infamous H&#8230;H bond in cis-butene<\/a>, one cannot just regard a bond as a purely localised phenomenon, one must also take into account what is happening elsewhere in the total system. Halogen bonds could also be regarding as filling the gap spanned by recognised covalency and recognised hydrogen bonds. I note in passing that another &#8220;awkward&#8221; bond is the <b>4th<\/b> in the diatomic C<sub>2<\/sub><span id=\"cite_ITEM-13105-3\" name=\"citation\"><a href=\"#ITEM-13105-3\">[4]<\/a><\/span> that has a bond energy of about 17 kcal\/mol, again weak for a normal bond and strong for an interaction.<\/p>\n<p>In my next post on this theme, I will deal with another halogen bond that is found in a famous molecule known for a long time and which has another weird property.<\/p>\n<hr \/>\n<p><sup>&Dagger;<\/sup>Postscript. An ELF analysis reveals the following basin centroids. Basin 1 integrates to 2.00 electrons, basin 2 to 1.92. The asymmetry in the position of the basin centroid towards the nitrogen suggests it is not an equally shared covalent bond, as indeed the Wiberg bond order noted above also indicates.  The I&#8230;I basin integrates to 1.86 electrons, indicating slightly reduced bonding (by donation into the  <em>sigma;<\/em> orbital).<br \/>\n<a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DABCO-I2-ELF1.jpg\"><img decoding=\"async\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DABCO-I2-ELF1.jpg\" alt=\"DABCO-I2-ELF\" width=\"400\"  class=\"aligncenter size-full wp-image-13151\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DABCO-I2-ELF1.jpg 1568w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DABCO-I2-ELF1-300x139.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/DABCO-I2-ELF1-1024x475.jpg 1024w\" sizes=\"(max-width: 1568px) 100vw, 1568px\" \/><\/a><\/p>\n<hr \/>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-13105-0\">Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., \"CCDC 879935: Experimental Crystal Structure Determination\", 2013. <a href=\"https:\/\/doi.org\/10.5517\/ccyjn03\">https:\/\/doi.org\/10.5517\/ccyjn03<\/a>\n\n<\/li>\n<li id=\"ITEM-13105-1\">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\", <i>Crystal Growth &amp; Design<\/i>, vol. 12, pp. 4157-4169, 2012. <a href=\"https:\/\/doi.org\/10.1021\/cg300669t\">https:\/\/doi.org\/10.1021\/cg300669t<\/a>\n\n<\/li>\n<li id=\"ITEM-13105-2\">H.S. Rzepa, \"Gaussian Job Archive for C12H24I8N4\", 2014. <a href=\"https:\/\/doi.org\/10.6084\/m9.figshare.1254779\">https:\/\/doi.org\/10.6084\/m9.figshare.1254779<\/a>\n\n<\/li>\n<li id=\"ITEM-13105-3\">D. Danovich, P.C. Hiberty, W. Wu, H.S. Rzepa, and S. Shaik, \"The Nature of the Fourth Bond in the Ground State of C&lt;sub&gt;2&lt;\/sub&gt;: The Quadruple Bond Conundrum\", <i>Chemistry \u2013 A European Journal<\/i>, vol. 20, pp. 6220-6232, 2014. <a href=\"https:\/\/doi.org\/10.1002\/chem.201400356\">https:\/\/doi.org\/10.1002\/chem.201400356<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 13105 -->","protected":false},"excerpt":{"rendered":"<p>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 a &#8220;non-covalent-interaction&#8221; (NCI) or not. [&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":[4],"tags":[1297,1035,924],"ppma_author":[2661],"class_list":["post-13105","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-bond-energy","tag-co-operative","tag-donor-acceptor-interaction-energy"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Halogen bonds 2: The DABCO-Iodine structure. - 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=13105\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Halogen bonds 2: The DABCO-Iodine structure. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"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 a &#8220;non-covalent-interaction&#8221; (NCI) or not. [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2014-11-30T16:56:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2014-12-03T16:49:42+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.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=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Halogen bonds 2: The DABCO-Iodine structure. - 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=13105","og_locale":"en_GB","og_type":"article","og_title":"Halogen bonds 2: The DABCO-Iodine structure. - Henry Rzepa&#039;s Blog","og_description":"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 a &#8220;non-covalent-interaction&#8221; (NCI) or not. [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2014-11-30T16:56:13+00:00","article_modified_time":"2014-12-03T16:49:42+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Halogen bonds 2: The DABCO-Iodine structure.","datePublished":"2014-11-30T16:56:13+00:00","dateModified":"2014-12-03T16:49:42+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105"},"wordCount":823,"commentCount":5,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.jpg","keywords":["bond energy","co-operative","donor-acceptor interaction energy"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105","name":"Halogen bonds 2: The DABCO-Iodine structure. - Henry Rzepa&#039;s Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.jpg","datePublished":"2014-11-30T16:56:13+00:00","dateModified":"2014-12-03T16:49:42+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=13105#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105#primaryimage","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.jpg","contentUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/11\/HEKZOO.jpg","width":992,"height":416,"caption":"Click for 3D"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13105#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"Halogen bonds 2: The DABCO-Iodine structure."}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa&#039;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\/pDef7-3pn","jetpack-related-posts":[{"id":13083,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13083","url_meta":{"origin":13105,"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 &quot;crystal_structure_mining&quot;","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":13105,"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 &quot;crystal_structure_mining&quot;","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":13136,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13136","url_meta":{"origin":13105,"position":2},"title":"Halogen bonds 3: &#8220;Nitrogen tri-iodide&#8221;","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 &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":16889,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16889","url_meta":{"origin":13105,"position":3},"title":"More stereoelectronics galore: hexamethylene triperoxide diamine.","author":"Henry Rzepa","date":"September 22, 2016","format":false,"excerpt":"Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news\u00a0and\u00a0known as HMTD (hexamethylene triperoxide diamine).\u00a0The crystal structure was reported some time ago and the article included an inspection of the computed wavefunction. However this did not\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":"hmtd","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/HMTD-1024x986.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24019,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24019","url_meta":{"origin":13105,"position":4},"title":"More record breakers for the anomeric effect involving C-N bonds.","author":"Henry Rzepa","date":"September 4, 2021","format":false,"excerpt":"An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom. A variation is to replace one oxygen by a nitrogen atom, as in N-C-O. Shown below is a scatter plot of the two distances to the common carbon atom derived from crystal structures.\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","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\/07\/N-C-O-distances-1024x758.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":21726,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21726","url_meta":{"origin":13105,"position":5},"title":"Hydrogen bonds: carbon as an acceptor rather than as a donor?","author":"Henry Rzepa","date":"December 23, 2019","format":false,"excerpt":"A hydrogen bond donor is considered as an electronegative element carrying a hydrogen that is accepted by an atom carrying a lone pair of electrons, as in X:...H-Y where X: is the acceptor and H-Y the donor. Wikipedia asserts that carbon can act as a donor, as we saw in\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/12\/query-1024x598.jpg?resize=350%2C200&ssl=1","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","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\/13105","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=13105"}],"version-history":[{"count":30,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/13105\/revisions"}],"predecessor-version":[{"id":13155,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/13105\/revisions\/13155"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=13105"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=13105"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=13105"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=13105"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}