{"id":18975,"date":"2017-11-07T13:40:47","date_gmt":"2017-11-07T13:40:47","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18975"},"modified":"2017-11-21T13:00:26","modified_gmt":"2017-11-21T13:00:26","slug":"hypervalence-revisited-the-odd-case-of-hexamethyl-selenium","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18975","title":{"rendered":"Hypervalence revisited. The odd case of hexamethyl selenium."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"18975\">\n<p>One thread that <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?cat=7\">runs through this blog<\/a> is that of <em><strong>hypervalency<\/strong><\/em>. It was therefore nice to come across a recent review of the concept<span id=\"cite_ITEM-18975-0\" name=\"citation\"><a href=\"#ITEM-18975-0\">[1]<\/a><\/span> which revisits the topic, and where a helpful summary is given of the evolving meanings over time of the term hypervalent. The key phrase &#8220;<em>it soon became clear that the two principles of the 2-centre-2-electron bond and the octet rule were sometimes in conflict<\/em>&#8221; succinctly summarises the issue. Two molecules that are discussed in this review caught my eye, CLi<sub>6<\/sub> and SeMe<sub>6<\/sub>. The former is stated as &#8220;<em>anomalous in terms of the Lewis model<\/em>&#8220;, but as I have shown in <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10801\">an earlier post<\/a>, the carbon is in fact not anomalous in a Lewis sense because of a large degree of Li-Li bonding. When this is taken into account, the Lewis model of the carbon becomes more &#8220;normal&#8221;. Here I take a look at the other cited molecule, SeMe<sub>6<\/sub>.<\/p>\n<p>I should start by summarising what I think are two fundamental ways in which electrons can be added to the valence shell of a main group element.<\/p>\n<ul>\n<li>If an s\/p basis only is used for the (main group) valence shell, then once eight electrons have populated the four bonding molecular orbitals constructed from this basis, additional electrons can then go into the four antibonding orbitals. This simple concept is often taught as an explanation for why the bond orders across the range N\u2261N, O=O, F-F and Ne&#8230;Ne decrease regularly (in fact one could also add CC to the left of this series, which is thought to have a weak quadruple bond). The Lewis octet is maintained throughout.<\/li>\n<li>The second fundamental possibility is to expand the valence shell basis set to s\/p\/d or s\/s\/p\/p (the second s or p-shell is the Rydberg level, <em>i.e.<\/em> 3s for carbon) or even s\/s\/p\/p\/d. That would be a true Lewis octet expansion, which depends on identifying significant Rydberg occupancy. This latter is in fact very rare, and few examples have been conclusively identified. One such as been <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15823\">discussed on this blog\u00a0<\/a> and more examples were presented at the <a href=\"http:\/\/dipc.ehu.es\/bondslam\/index.php\/Hypervalence\">Aachen bond Slam<\/a> in September 2017. Unlike the first mechanism (which reduces bond orders), this one actually increases bond orders and any bonds where the atomic orbital contributions have a significant Rydberg component can be considered as &#8220;<strong><em>Hyperbonds<\/em><\/strong>&#8220;.<\/li>\n<\/ul>\n<p>One can then address the issue of hypervalency (and any octet expansion) by analysing the basis set contributions of the orbitals. These orbitals can be either canonical molecular orbitals or localised (NBO) orbitals. If a single determinant wavefunction is appropriate, then the orbitals would be doubly occupied (for closed shell species). If the molecule has multi-reference character, then of course fractional electron occupancy of these orbitals may be required (as would <em>e.g.<\/em> be the case for ozone, O<sub>3<\/sub>, another molecule asserted in the review as hypervalent<span id=\"cite_ITEM-18975-0\" name=\"citation\"><a href=\"#ITEM-18975-0\">[1]<\/a><\/span>).<\/p>\n<p>There are other ways of analysing the wavefunction. The one discussed at length in the review<span id=\"cite_ITEM-18975-0\" name=\"citation\"><a href=\"#ITEM-18975-0\">[1]<\/a><\/span> is from an atomic charge map, but also mentioned is an ELF partitioning. This derives not from an orbital population but from the distribution of a function (ELF) calculated from the electron density itself. It was this latter method that was cited for\u00a0SeMe<sub>6<\/sub>. The ELF method partitions electrons into so-called basins, which can be monosynaptic (lone pairs and ionic bonds), disynaptic (covalent bonds) and more rarely trisynaptic (3-centre bonds). Using this analysis, six disynaptic octahedrally-arranged ELF basins were located for\u00a0\u00a0SeMe<sub>6\u00a0<\/sub>\u00a0(&#8220;<em>in which the Se\u2013C bonds are relatively\u00a0non-polar, can have electron populations exceeding 8 at the\u00a0central atom&#8221;<\/em><span id=\"cite_ITEM-18975-0\" name=\"citation\"><a href=\"#ITEM-18975-0\">[1]<\/a><\/span>) and for which the total integration cames to 11.34e (FAIR Data DOI for this calculation can be see at\u00a0<a href=\"https:\/\/doi.org\/10.14469\/hpc\/3219\">10.14469\/hpc\/3219<\/a>).<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-18979\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/165-1024x1008.jpg\" alt=\"\" width=\"450\" height=\"443\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/165-1024x1008.jpg 1024w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/165-300x295.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/165-768x756.jpg 768w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/165.jpg 1040w\" sizes=\"auto, (max-width: 450px) 100vw, 450px\" \/>The key phrase is &#8220;non-polar&#8221;, since the Lewis concept relates to shared electron pair or covalent hypervalency. It was this aspect that I focused on seven years back in looking at whether <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=2687\">e.g. IF<sub>7<\/sub><\/a> was hypervalent (along with\u00a0I(CN)<sub>7<\/sub>). These were too ionic to reveal disynaptic covalent ELF basins. So in an effort to reduce the polarity, I tried II<sub>7<\/sub> and At.At<sub>7<\/sub>, on the grounds that these homonuclear molecules might be less polar. The seven I-I or At-At ELF disynaptic basins integrated to totals of 6.55 and 6.47e respectively; there was no evidence of &#8220;octet expansion&#8221; for either central halogen. Instead of course, the six electrons in the octet-excess needed to create seven I-I bonds actually populate I-I antibonding orbitals, as per method 1 above. Accordingly the I-I bond orders reduce from 1.0 to <em>e.g.<\/em> 0.47 for the axial substituents and 0.37 for the five equatorial groups.<\/p>\n<p><img decoding=\"async\" class=\"aligncenter size-full wp-image-18980\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/I8-elf.jpg\" alt=\"\" width=\"350\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/I8-elf.jpg 551w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/I8-elf-292x300.jpg 292w\" sizes=\"(max-width: 551px) 100vw, 551px\" \/><\/p>\n<p>One interesting property of the centroid of the ELF basins is that you can infer the polarity of the bond from its position along the bond axis. For\u00a0II<sub>7<\/sub>,<sub>\u00a0<\/sub>the centroids are displaced towards the central iodine, indicating it is more electronegative, and away from the terminal iodine, indicating it is the electropositive partner. I mention this since the ELF basins for SeMe<sub>6<\/sub> show the centroids to be strongly displaced <strong>towards<\/strong> the carbon and away from the Se (0.38\/0.62), indicating that this molecule is in fact polar and NOT non-polar as was asserted.\u00a0<\/p>\n<p>To follow-up this latter observation, I did an NBO analysis of the wavefunction for\u00a0SeMe<sub>6<\/sub> (FAIR Data DOI:\u00a0<a href=\"https:\/\/doi.org\/10.14469\/hpc\/3220\">10.14469\/hpc\/3220<\/a>). This reveals the following properties.<\/p>\n<ul>\n<li>Se populations: [core]4S( 1.30)4p( 3.04)4d( 0.06)5p( 0.01) of which Rydberg = 0.06516, natural charge on Se,\u00a01.60224<\/li>\n<li>C populations:\u00a0\u00a0[core]2S( 1.20)2p( 3.65)3S( 0.01)3p( 0.01) of which Rydberg = 0.01838, natural charge on C\u00a0-0.86670<\/li>\n<li>H populations:\u00a0\u00a01S( 0.80)<\/li>\n<li>Total Rydberg population: 0.20556<\/li>\n<li>Wiberg Se-C bond orders:\u00a0\u00a00.6689<\/li>\n<li>Wiberg bond indices:\u00a0\u00a0Se 4.0431,\u00a0C 3.8252,\u00a0\u00a0H 0.9621<\/li>\n<\/ul>\n<p>So according to this orbital-based analysis,\u00a0SeMe<sub>6<\/sub>\u00a0is in effect a partially ionic compound with no evidence of significant Rydberg occupancies and hence no evidence of any octet expansion at Se. Thus we see two different interpretations emerging, depending on the analytical method used:<\/p>\n<ol>\n<li>SeMe<sub>6\u00a0<\/sub>is a polar molecule with no hypervalent attributes as judged using orbital analysis.<\/li>\n<li>As a polar molecule, it has six methyl carbanion-like substituents in which the carbon &#8220;lone pairs&#8221; all point towards the Se, manifesting as disynaptic ELF basins and indicating a total valence-basin octet-expanded population of 11.34e at Se. Even though this octet expansion originates mostly from the carbon atomic orbitals, the disynaptic nature of these valence basins means that the Se could indeed be defined as hypervalent.<\/li>\n<\/ol>\n<p>Well,\u00a0SeMe<sub>6<\/sub> has turned out to be rather less clear-cut than implied<em>\u00a0by <\/em>the assertion<em> &#8220;in which the Se\u2013C bonds are relatively\u00a0non-polar&#8221;. <\/em>There are however possible modifications to\u00a0SeMe<sub>6<\/sub> that might yet make it less polar. These may be the subject of a follow-up post.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-18975-0\">M.C. Durrant, \"A quantitative definition of hypervalency\", <i>Chemical Science<\/i>, vol. 6, pp. 6614-6623, 2015. <a href=\"https:\/\/doi.org\/10.1039\/c5sc02076j\">https:\/\/doi.org\/10.1039\/c5sc02076j<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 18975 -->","protected":false},"excerpt":{"rendered":"<p>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 &#8220;it soon became clear that the two [&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":[7],"tags":[557,2275,1679,1630],"ppma_author":[2661],"class_list":["post-18975","post","type-post","status-publish","format-standard","hentry","category-hypervalency","tag-chemical-bonding","tag-city-aachen","tag-hypervalent-molecule","tag-molecular-geometry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Hypervalence revisited. The odd case of hexamethyl selenium. - 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=18975\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Hypervalence revisited. The odd case of hexamethyl selenium. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"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 &#8220;it soon became clear that the two [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18975\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-11-07T13:40:47+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-11-21T13:00:26+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/11\/165-1024x1008.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=\"6 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Hypervalence revisited. The odd case of hexamethyl selenium. - 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=18975","og_locale":"en_GB","og_type":"article","og_title":"Hypervalence revisited. The odd case of hexamethyl selenium. - Henry Rzepa&#039;s Blog","og_description":"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. 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It was a spectacular vindication of the earlier\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"Click for  3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/CLi6-Lp.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19194,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19194","url_meta":{"origin":18975,"position":1},"title":"Identification of a simplest hypervalent hydrogen fluoride anion.","author":"Henry Rzepa","date":"December 8, 2017","format":false,"excerpt":"An article with the title shown above in part recently appeared. Given the apparent similarity of HF1- to CH3F1- and CH3F2-, the latter of which I introduced on this blog previously,\u00a0I thought it of interest to apply my analysis to HF1-. The authors conclude that \"the F atom of HF\u2212\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":19279,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19279","url_meta":{"origin":18975,"position":2},"title":"Can any hypervalence in diazomethanes be amplified?","author":"Henry Rzepa","date":"December 23, 2017","format":false,"excerpt":"In the previous post, I referred to a recently published review on hypervalency which introduced a very simple way (the\u00a0valence electron equivalent \u03b3)\u00a0of quantifying the effect.\u00a0Diazomethane was cited as one example of a small molecule exhibiting hypervalency (on nitrogen) by this measure. Here I explore the effect of substituting diazomethane\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2599,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2599","url_meta":{"origin":18975,"position":3},"title":"Hypervalency: Is it real?","author":"Henry Rzepa","date":"October 16, 2010","format":false,"excerpt":"The Wikipedia page on hypervalent compounds reveals that the concept is almost as old as that of normally valent compounds. The definition there, \u00a0is \"a molecule that contains one or more\u00a0main group elements formally bearing more than eight\u00a0electrons in their\u00a0valence shells\" (although it could equally apply to e.g. transition elements\u2026","rel":"","context":"In &quot;Hypervalency&quot;","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\/10\/IH7.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":15823,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15823","url_meta":{"origin":18975,"position":4},"title":"Real hypervalency in a small molecule.","author":"Henry Rzepa","date":"February 21, 2016","format":false,"excerpt":"Hypervalency is defined as a molecule\u00a0that contains one or more main group elements formally bearing more than eight\u00a0 electrons in their\u00a0 valence shell. One example of a molecule so characterised was CLi6 where the description \"\u201ccarbon can expand its octet of electrons to form this relatively stable molecule\u201c was used.\u2026","rel":"","context":"In &quot;Bond slam&quot;","block_context":{"text":"Bond slam","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2237"},"img":{"alt_text":"CH4","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/02\/CH4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19307,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19307","url_meta":{"origin":18975,"position":5},"title":"Are diazomethanes hypervalent molecules? An attempt into more insight by more &#8220;tuning&#8221; with substituents.","author":"Henry Rzepa","date":"December 26, 2017","format":false,"excerpt":"Recollect the suggestion\u00a0that diazomethane has hypervalent character. When I looked into this, I came to the conclusion that it probably was mildly hypervalent, but on carbon and not nitrogen. Here I try some variations with substituents to see what light if any this casts. I have expanded the resonance forms\u2026","rel":"","context":"In &quot;Hypervalency&quot;","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\/12\/H2CNCCN_ELF-1024x258.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","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\/18975","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=18975"}],"version-history":[{"count":11,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18975\/revisions"}],"predecessor-version":[{"id":18989,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18975\/revisions\/18989"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18975"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18975"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18975"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18975"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}