{"id":18632,"date":"2017-07-18T09:03:11","date_gmt":"2017-07-18T08:03:11","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18632"},"modified":"2017-07-18T09:03:11","modified_gmt":"2017-07-18T08:03:11","slug":"dispersion-bonds-not-involving-just-hydrogen-can-it-work-for-f-h","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632","title":{"rendered":"Dispersion \u201cbonds\u201d not involving just hydrogen: can it work for F…H?"},"content":{"rendered":"
\n

The effects of loading up lots of dispersion attractions (between t-butyl groups) into a compact molecule has the interesting consequence of allowing two “non-bonded” hydrogen atoms to approach to ~1.5\u00c5 of each other, thus creating the appearance of a “bond” where one normally would not be found. Can such an effect be injected into other combinations of two atoms, say H and F? Here I briefly explore this notion.<\/p>\n

The system is a slightly modified version of the one[1]<\/a><\/span> already studied; R3<\/sub>C-F…H-CR3<\/sub> (R=3,5-bis-t-butylphenyl), and a B3LYP+D3BJ\/6-311G(d,p) calculation\u2021<\/sup> (with C3<\/sub>-symmetry imposed) shows (DOI: 10.14469\/hpc\/2734<\/a>)\u00a0the following, with the key atom pair distances shown below. Note the abnormally short F…H distance, and the relatively long C-F one.<\/p>\n

\"\"<\/p>\n

Note the casual phrase “C3<\/sub>-symmetry imposed”. This is a little “shortcut” one can try to use to shorten the calculation time. I should explain that on our computer system here, we are allowed a maximum of 72 hours per calculation. I already suspected that without the use of such symmetry the calculation would take longer and so used symmetry to “fit the calculation in” to this time slot. In the event it took 55 hours. There is a simple test however to see if this shortcut is justified; does the resulting molecule have 3N-6 real normal vibrational modes (i.e. ones with +ve force constants)? In fact this system fails this test; two of these modes have small negative force constants, corresponding to\u00a0\u03bd -11 cm-1<\/sup>. You might think this is small enough to perhaps attribute to e.g.<\/em> the use of too-small a basis set or some other computational imperfection. Actually, although\u00a0-11 cm-1<\/sup> is numerically small, the mass-weighting associated with the vibration is in effect the entire system (below) and hence this mode is indeed significant.<\/p>\n

\"\"<\/p>\n

So time to release the symmetry and when one does this an entirely different geometry emerges (DOI:\u00a010.14469\/hpc\/2736<\/a>) for which now all the 3N-6 normal modes have +ve force constants.<\/p>\n

\"\"<\/p>\n

The “non-bonded” F…H interaction is now considerably longer, although still ~0.5\u00c5 shorter than the sum of the van der Waals radii (~2.65\u00c5). This F…H non-bonded distance shows up as below in the Cambridge structure database (CSD) distribution. This suggests the shortest interaction is indeed ~2.1\u00c5. The string of isolated examples with shorter distances down to < 1\u00c5 are very likely all crystallographic artefacts or errors.<\/p>\n

\"\"<\/p>\n

So we may conclude that using the same system that was so successfully used to demonstrate the dispersion-induced ultra-short H…H distance cannot be modified to produce any such extreme effects in the F…H pair. \u00a0Perhaps indeed “dispersion bonds” will always be limited to \u00a0H…H pairs.<\/p>\n

\n

\u2021<\/sup> When this method is used for the original H…H system, it yields a H…H distance of 1.529\u00c5 for which all the normal vibrational modes are real; DOI: 10.14469\/hpc\/2739<\/a>).<\/p>\n

References<\/h2>\n
  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\", Journal of the American Chemical Society<\/i>, vol. 139, pp. 7428-7431, 2017. https:\/\/doi.org\/10.1021\/jacs.7b01879<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    The effects of loading up lots of dispersion attractions (between t-butyl groups) into a compact molecule has the interesting consequence of allowing two “non-bonded” hydrogen atoms to approach to ~1.5\u00c5 of each other, thus creating the appearance of a “bond” where one normally would not be found. Can such an effect be injected into other […]<\/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":[],"ppma_author":[2661],"class_list":["post-18632","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nDispersion \u201cbonds\u201d not involving just hydrogen: can it work for F...H? - 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=18632\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Dispersion \u201cbonds\u201d not involving just hydrogen: can it work for F...H? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The effects of loading up lots of dispersion attractions (between t-butyl groups) into a compact molecule has the interesting consequence of allowing two “non-bonded” hydrogen atoms to approach to ~1.5\u00c5 of each other, thus creating the appearance of a “bond” where one normally would not be found. Can such an effect be injected into other […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-07-18T08:03:11+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/07\/227.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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Dispersion \u201cbonds\u201d not involving just hydrogen: can it work for F...H? - 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=18632","og_locale":"en_GB","og_type":"article","og_title":"Dispersion \u201cbonds\u201d not involving just hydrogen: can it work for F...H? - Henry Rzepa's Blog","og_description":"The effects of loading up lots of dispersion attractions (between t-butyl groups) into a compact molecule has the interesting consequence of allowing two “non-bonded” hydrogen atoms to approach to ~1.5\u00c5 of each other, thus creating the appearance of a “bond” where one normally would not be found. Can such an effect be injected into other […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632","og_site_name":"Henry Rzepa's Blog","article_published_time":"2017-07-18T08:03:11+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/07\/227.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Dispersion \u201cbonds\u201d not involving just hydrogen: can it work for F…H?","datePublished":"2017-07-18T08:03:11+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632"},"wordCount":488,"commentCount":3,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/07\/227.jpg","articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632","name":"Dispersion \u201cbonds\u201d not involving just hydrogen: can it work for F...H? - 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=18632#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/07\/227.jpg","datePublished":"2017-07-18T08:03:11+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=18632#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632#primaryimage","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/07\/227.jpg","contentUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/07\/227.jpg","width":926,"height":420},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18632#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"Dispersion \u201cbonds\u201d not involving just hydrogen: can it work for F…H?"}]},{"@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\/pDef7-4Qw","jetpack-related-posts":[{"id":22231,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22231","url_meta":{"origin":18632,"position":0},"title":"A molecular sponge for hydrogen storage- the future for road transport?","author":"Henry Rzepa","date":"April 19, 2020","format":false,"excerpt":"In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus \"NU-1501-Al\" can absorb 14 weight% of hydrogen. To power a low-polluting car with a 500 km range, about\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\/2020\/04\/MOF1-1024x990.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":14718,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14718","url_meta":{"origin":18632,"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 "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":20576,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20576","url_meta":{"origin":18632,"position":2},"title":"The shortest known CF…HO hydrogen bond.","author":"Henry Rzepa","date":"March 24, 2019","format":false,"excerpt":"There is a predilection amongst chemists for collecting records; one common theme is the length of particular bonds, either the shortest or the longest. A particularly baffling type of bond is that between the very electronegative F atom and an acid hydrogen atom such as that in OH. Thus short\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\/2019\/03\/F-inter-300x189.png?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":18582,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18582","url_meta":{"origin":18632,"position":3},"title":"Dispersion “bonds” not involving hydrogen. A Cl…Cl candidate?","author":"Henry Rzepa","date":"June 29, 2017","format":false,"excerpt":"In the previous post, I noted the crystallographic detection of an unusually short non-bonded H...H contact of ~1.5\u00c5, some 0.9\u00c5 shorter than twice the van der Waals radius of hydrogen (1.2\u00c5, although some sources quote 1.1\u00c5 which would make the contraction ~0.7\u00c5). This was attributed to dispersion attractions accumulating in\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":23134,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23134","url_meta":{"origin":18632,"position":4},"title":"Global aromaticity at the nanoscale.","author":"Henry Rzepa","date":"December 31, 2020","format":false,"excerpt":"Here is another of the \"large\" molecules in the c&e news shortlist for molecule-of-the-year, 2020. This one is testing the H\u00fcckel 4n+2 rule out to a value never before seen (n = 40, or 162 \u03c0-electrons). The take-home message is that this rule seems to behave well in predicting global\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/12\/c-P6e6_neutral.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":18632,"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 "Interesting chemistry"","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\/18632","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=18632"}],"version-history":[{"count":8,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18632\/revisions"}],"predecessor-version":[{"id":18644,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18632\/revisions\/18644"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18632"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18632"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18632"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18632"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}