{"id":18555,"date":"2017-06-26T17:39:02","date_gmt":"2017-06-26T16:39:02","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18555"},"modified":"2017-06-30T13:41:41","modified_gmt":"2017-06-30T12:41:41","slug":"dispersion-bonds-a-new-example-with-an-ultra-short-h-h-distance","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18555","title":{"rendered":"Dispersion &#8220;bonds&#8221;: a new example with an ultra-short H&#8230;H distance."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"18555\">\n<p>About 18 months ago, there was <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=11331\">much discussion<\/a>\u00a0on this blog about a system reported by Bob Pascal and co-workers containing a short H&#8230;H contact of ~1.5\u00c5<span id=\"cite_ITEM-18555-0\" name=\"citation\"><a href=\"#ITEM-18555-0\">[1]<\/a><\/span>. In this system, the hydrogens were both attached to Si as Si-H&#8230;H-Si and compressed together by rings. Now a new report<span id=\"cite_ITEM-18555-1\" name=\"citation\"><a href=\"#ITEM-18555-1\">[2]<\/a><\/span> and\u00a0<a href=\"http:\/\/comporgchem.com\/blog\/?p=4014\">commented upon by Steve Bachrach<\/a>, claims a similar distance for hydrogens attached to carbon,<em> i.e.<\/em> C-H&#8230;H-C, but without the ring compression.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-18559\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/06\/201-1024x987.jpg\" alt=\"\" width=\"450\" height=\"434\" \/><\/p>\n<p>This new example is the structure of an C<sub>3<\/sub>-symmetric all-meta <sup><i>t<\/i><\/sup>Bu-triphenylmethane R-H&#8230;H-R dimer determined by neutron diffraction (DOI: <a href=\"https:\/\/dx.doi.org\/10.5517\/ccdc.csd.cc1nc1bd\">10.5517\/ccdc.csd.cc1nc1bd<\/a>) and the close interaction is achieved purely by attractions due to dispersion forces accumulating in the remainder of the molecules. This study also reports a diverse set of computed properties for this new system, but one property reported as part of the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=11331\">previous discussion<\/a> was not presented, the\u00a0<sup>1<\/sup>J<sub>H-H<\/sub> coupling constant. I have computed it here in the hope that it might be possible to measure by some means, perhaps in the solid state?<\/p>\n<p>The chemical shift of the R<sub>3<\/sub>CH proton is measured as a singlet<sup>\u2021<\/sup> at ~7.35 ppm (in deuterated benzene, Figure S6, SI).<sup>\u2020<\/sup>\u00a0<img decoding=\"async\" class=\"aligncenter size-full wp-image-18570\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/06\/NMR.jpg\" alt=\"\" width=\"300\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/06\/NMR.jpg 618w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/06\/NMR-300x281.jpg 300w\" sizes=\"(max-width: 618px) 100vw, 618px\" \/><\/p>\n<p>The value calculated using B3LYP\/Def2-TZVPP (gas phase) is 7.39 and 7.69 ppm (averaged to 7.54 for a rapidly exchanging environment). The<sup> 1<\/sup>J coupling is calculated as 4.3 Hz at the B3LYP\/Def2-TZVPP level, DOI: <a href=\"https:\/\/doi.org\/10.14469\/hpc\/2699\">10.14469\/hpc\/2699<\/a>. The designation\u00a0<sup>1<\/sup>J is normally taken as a 1-bond pathway for the coupling. In this example, the designation of the H-H region as a &#8220;bond&#8221; is the interesting discussion point!<\/p>\n<p>I end by noting here <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17579\">my observation<\/a> that although the neutron diffraction study of ammonium tetraphenylborate shows the \u00a0N-H protons as pointing directly towards the centroid of phenyl groups, the original observation<span id=\"cite_ITEM-18555-2\" name=\"citation\"><a href=\"#ITEM-18555-2\">[3]<\/a><\/span> was made that &#8220;e<em>ven at 20 K the ammonium ion performs large amplitude motions which allow the N-H vectors to sample the entire face of the aromatic system&#8221;. \u00a0<\/em>The equivalent thermal motion for the triphenylmethane system here would have the \u00a0C-H vectors orbiting around each other in a manner that increases the H-H separation, but which averages out to them pointing directly towards one another? \u00a0The calculated normal coordinate analysis of this system is not available from the article SI, so the ease of \u00a0C-C-H bending to achieve such motion is difficult to ascertain. Perhaps trying to detect the\u00a0<sup>1<\/sup>J coupling might illuminate whether this happens?<\/p>\n<hr \/>\n<p><b>Postscript<\/b>. <sup>\u2020<\/sup>Prof Schreiner has indicated that that the methine assignment is 5.79 ppm (<b>b<\/b> below) and not 7.35 as marked with a diamond in the S6 figure caption (<strong>a<\/strong> below). This is of course measured in d6-benzene solution and applies to the monomer, not presumably the dimer. The calculated value of 7.54 ppm as reported above applies specifically to the dimer, which suggests a significant shift of ~2ppm upon dimer formation. It would be interesting to verify this prediction <i>via<\/i> a solid-state measurement. <br \/>\n <img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-18621\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/06\/135-1024x565.jpg\" alt=\"\" width=\"450\" height=\"248\" \/><\/p>\n<hr \/>\n<p><sup>\u2021<\/sup><small>Measuring coupling would require an asymmetric environment to differentiate the two chemical shifts of the interacting hydrogens. Although the C<sub>3<\/sub> symmetry of the crystal structure could provide such an environment, it is observed to be fluxional in solution, \u00a0which equalises the two chemical shifts on the NMR time scale. Two non-equivalent protons exhibiting only mutual couplings manifest as an AB-type double doublet of peaks in the NMR spectrum. As the difference in chemical shift between the two nuclei (in units of Hz) approaches in magnitude the value of the coupling constant between them (also in Hz), the AB quartet becomes increasingly second-order in appearance. This means that the intensities of the two outer peaks starts to decrease and the two inner peak intensities increase. When the chemical shift difference between them reaches zero, the intensity of the two outer peaks also becomes zero and the two inner peaks superimpose to become a single peak. This means that the coupling constant cannot be measured from the splitting of the peaks (which has vanished). It does <b>not<\/b> mean of course that the coupling itself has vanished; it merely no longer manifests in the spectrum.<\/small><\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-18555-0\">J. Zong, J.T. Mague, and R.A. Pascal, \"Exceptional Steric Congestion in an &lt;i&gt;in&lt;\/i&gt;,&lt;i&gt;in&lt;\/i&gt;-Bis(hydrosilane)\", <i>Journal of the American Chemical Society<\/i>, vol. 135, pp. 13235-13237, 2013. <a href=\"https:\/\/doi.org\/10.1021\/ja407398w\">https:\/\/doi.org\/10.1021\/ja407398w<\/a>\n\n<\/li>\n<li id=\"ITEM-18555-1\">S. R\u00f6sel, H. Quanz, C. Logemann, J. Becker, E. Mossou, L. Ca\u00f1adillas-Delgado, E. Caldeweyher, S. Grimme, and P.R. Schreiner, \"London Dispersion Enables the Shortest Intermolecular Hydrocarbon H\u00b7\u00b7\u00b7H Contact\", <i>Journal of the American Chemical Society<\/i>, vol. 139, pp. 7428-7431, 2017. <a href=\"https:\/\/doi.org\/10.1021\/jacs.7b01879\">https:\/\/doi.org\/10.1021\/jacs.7b01879<\/a>\n\n<\/li>\n<li id=\"ITEM-18555-2\">T. Steiner, and S.A. Mason, \"Short N&lt;sup&gt;+&lt;\/sup&gt;\u2014H...Ph hydrogen bonds in ammonium tetraphenylborate characterized by neutron diffraction\", <i>Acta Crystallographica Section B Structural Science<\/i>, vol. 56, pp. 254-260, 2000. <a href=\"https:\/\/doi.org\/10.1107\/s0108768199012318\">https:\/\/doi.org\/10.1107\/s0108768199012318<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 18555 -->","protected":false},"excerpt":{"rendered":"<p>About 18 months ago, there was much discussion\u00a0on this blog about a system reported by Bob Pascal and co-workers containing a short H&#8230;H contact of ~1.5\u00c5. In this system, the hydrogens were both attached to Si as Si-H&#8230;H-Si and compressed together by rings. Now a new report and\u00a0commented upon by Steve Bachrach, claims a similar [&hellip;]<\/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":[4],"tags":[905,2235,237,2236,49,145,1439,20],"ppma_author":[2661],"class_list":["post-18555","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-10-1021","tag-blog","tag-chemical-shift","tag-chemical-shift-difference","tag-chemical-shifts","tag-gas-phase","tag-oxygen","tag-steve-bachrach"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Dispersion &quot;bonds&quot;: a new example with an ultra-short H...H distance. - 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=18555\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Dispersion &quot;bonds&quot;: a new example with an ultra-short H...H distance. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"About 18 months ago, there was much discussion\u00a0on this blog about a system reported by Bob Pascal and co-workers containing a short H&#8230;H contact of ~1.5\u00c5. In this system, the hydrogens were both attached to Si as Si-H&#8230;H-Si and compressed together by rings. 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It had been inferred from the X-ray structure that the H...H distance was in the region of 1.50\u00c5. It's that cis-butene all\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":"Si","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/10\/Si.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14718,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14718","url_meta":{"origin":18555,"position":1},"title":"Interactions responsible for the lowest energy structure of the trimer of fluoroethanol.","author":"Henry Rzepa","date":"October 23, 2015","format":false,"excerpt":"Steve Bachrach on his own blog has commented on a recent article discussing the structure of the trimer of fluoroethanol. Rather than the expected triangular form with three OH---O hydrogen bonds, the lowest energy form only had two such bonds, but it matched the microwave data much better. Here I\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":19347,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19347","url_meta":{"origin":18555,"position":2},"title":"Hypervalent hydrogen?","author":"Henry Rzepa","date":"January 13, 2018","format":false,"excerpt":"I discussed the molecule the molecule CH3F2- a while back. It was a very rare computed example of a system where the added two electrons populate the higher valence shells known as Rydberg orbitals as an alternative to populating the C-F antibonding \u03c3-orbital to produce CH3- and F-. The net\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":12583,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12583","url_meta":{"origin":18555,"position":3},"title":"Kekul\u00e9&#8217;s vibration: A modern example of its use.","author":"Henry Rzepa","date":"June 6, 2014","format":false,"excerpt":"Following the discussion here of Kekul\u00e9's suggestion of what we now call a vibrational mode (and which in fact now bears his name), I thought I might apply the concept to a recent molecule known as [2.2]paracyclophane. The idea was sparked by Steve Bachrach's latest post, where the \"zero-point\" structure\u2026","rel":"","context":"In &quot;Historical&quot;","block_context":{"text":"Historical","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=565"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":18205,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18205","url_meta":{"origin":18555,"position":4},"title":"\u03c0-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach?","author":"Henry Rzepa","date":"April 17, 2017","format":false,"excerpt":"Following on from my re-investigation of close hydrogen bonding contacts to the \u03c0-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469\/hpc\/2478) is similar to the previous one: QA is any of N,O,F,Cl. X is any atom, including metals and non-metals. The\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\/2017\/04\/triple-inter-1024x672.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":21407,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21407","url_meta":{"origin":18555,"position":5},"title":"Does Kekulene have Kekul\u00e9 vibrational modes? Yes!","author":"Henry Rzepa","date":"October 19, 2019","format":false,"excerpt":"Increasingly, individual small molecules are having their structures imaged using STM, including cyclo[18]carbon that I recently discussed. The latest one receiving such treatment is Kekulene. As with cyclo[18]carbon, the point of interest was which of the two resonance structures shown below most closely resembled the measured structure. The one on\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\/10\/b3-1423-B2u-1024x575.gif?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\/18555","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=18555"}],"version-history":[{"count":26,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18555\/revisions"}],"predecessor-version":[{"id":18627,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18555\/revisions\/18627"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18555"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18555"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18555"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18555"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}