{"id":18582,"date":"2017-06-29T09:24:40","date_gmt":"2017-06-29T08:24:40","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18582"},"modified":"2017-06-29T10:44:57","modified_gmt":"2017-06-29T09:44:57","slug":"dispersion-bonds-not-involving-hydrogen","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18582","title":{"rendered":"Dispersion “bonds” not involving hydrogen. A Cl…Cl candidate?"},"content":{"rendered":"
\n

In the previous post<\/a>, 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 the rest of the molecule. I asked myself what the potential might be for other elements to reveal significantly contracted non-bonded distances as a result of\u00a0dispersive attractions.<\/p>\n

Here is a simple search of the CSD (Cambridge structure database, query DOI: 10.14469\/hpc\/2700<\/a>) for the monovalent halogens as in C-X. The other constraints are R<0.05, no errors, no disorder, normalised hydrogen positions and a non-bonded intermolecular contacts \u22650.4\u00c5<\/strong> shorter than the sum of the van der Waals radii (a recent compendium of atomic values is available here[1]<\/a><\/span>). I should state at the outset that this sort of search for non-bonded contacts is quite effective at revealing errors in the crystallographic determination, despite the search request that there be none. None, that is, that have been identified; there are many that have not been! So this survey only aims to tease out any broad trends, rather than a specific focus on individual systems.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\n

Hits<\/p>\n<\/th>\n

Comments<\/th>\n<\/tr>\n
15,500<\/td>\nH…H, vdW sum = 2.4\u00c5; The accepted shortest H…H contacts are around 1.5\u00c5; it is likely the majority of entries (all?) with shorter values are crystallographic errors. There is a curious maximum at ~1.78\u00c5 which probably relates to the H…H non-bonded distance in CH2<\/sub> groups, despite the attempted constraint that the interaction be intermolecular<\/strong>.<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
31<\/td>\nF…F, vdW sum = 2.94\u00c5; there are few examples in total and even fewer with the non-bonded distance contracted by\u00a0\u22650.5\u00c5. Those with \u22650.8\u00c5 are probably crystal errors.<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
70<\/td>\nCl…Cl vdW sum =3.5\u00c5. Examples at distances of <2.0\u00c5 (a contraction of 1.5\u00c5) are almost certainly errors, even the contractions ~1.0\u00c5 are suspect. Does this however indicate Cl is more polarisable than F?<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
26<\/td>\nBr…Br vdW sum = 3.7\u00c5. Examples contracted by\u00a0\u22650.4\u00c5 are isolated (errors?).<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
10<\/td>\nI…I vdW sum = 3.96\u00c5. There are no examples contracted by \u22650.5\u00c5; shorter contractions are again errors?\u00a0<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
1164<\/td>\nH…F vdW sum = 2.67\u00c5. The separator between real values and probable errors is ~2.1\u00c5, which indicates contractions of \u00a00.6\u00c5 are probably real.<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
222<\/td>\nH…Cl vdW sum = 2.95\u00c5.\u00a0The separator between real values and probable errors is ~2.4\u00c5; contractions of \u00a0~0.5\u00c5 are probably real.<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
37<\/td>\nH…Br vdW sum = 3.05\u00c5.\u00a0The separator between real values and probable errors is ~2.8\u00c5; contractions of \u00a0~0.3\u00c5 are probably real.<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n
4<\/td>\nH…I vdW sum = 3.18\u00c5. More data is needed!<\/td>\n<\/tr>\n
\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

We see from these results that the number of short H…H contacts far exceeds those found for the halogen series.\u2021<\/sup> Clearly whilst the electron density surrounding H is low, that for the halogens is far higher and hence that electron repulsions are going to be far greater. The effect is attenuated if one partner is H itself, with van der Waals contractions in-between those for X…X \u00a0and H…H contacts.<\/p>\n

This brief survey suggests that \u00a0H…H distances are by far the best for probing close contacts brought about by dispersion attractions. Perhaps the next element to focus on for such effects might be chlorine rather than fluorine. For example, see DOI: 10.5517\/cczjyhx<\/a>, being Ph3<\/sub>C-Cl…Cl-CPh3<\/sub> where the Cl…Cl distance is contracted by ~0.3\u00c5. What would happen if the Ph groups were adorned with t-butyl groups to increase the dispersion attractions?<\/p>\n

\n

\u2021<\/sup> It might of course also mean that the van der Waals radius for H is set too high.<\/p>\n

References<\/h2>\n
  1. S. Alvarez, \"A cartography of the van der Waals territories\", Dalton Transactions<\/i>, vol. 42, pp. 8617, 2013. https:\/\/doi.org\/10.1039\/c3dt50599e<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    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 the rest of the molecule. […]<\/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":[1745],"tags":[],"ppma_author":[2661],"class_list":["post-18582","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining"],"yoast_head":"\nDispersion "bonds" not involving hydrogen. A Cl...Cl candidate? - 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=18582\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Dispersion "bonds" not involving hydrogen. A Cl...Cl candidate? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 the rest of the molecule. 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Can such an\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\/2017\/07\/230-1024x551.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":21096,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21096","url_meta":{"origin":18582,"position":1},"title":"CH…O hydrogen bonding competing with layered dispersion attractions.","author":"Henry Rzepa","date":"July 19, 2019","format":false,"excerpt":"I have previously looked at the topic of hydrogen bonding interactions from the hydrogen of chloroform Here I generalize\u00a0C-H...O interactions by conducting searches of the CSD (Cambridge structure database) as a function of the carbon hybridisation.\u00a0I am going to jump straight to a specific molecule XEVJIR (DOI: 10.5517\/cc5fgpq) identified from\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\/07\/XEVJIR-1024x839.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":1856,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1856","url_meta":{"origin":18582,"position":2},"title":"Conformational analysis of biphenyls: an upside-down view","author":"Henry Rzepa","date":"April 2, 2010","format":false,"excerpt":"One of the (not a few) pleasures of working in a university is the occasional opportunity that arises to give a new lecture course to students. New is not quite the correct word, since the topic I have acquired is Conformational analysis. The original course at Imperial College was delivered\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\/2010\/04\/biphenyl-1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17579,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","url_meta":{"origin":18582,"position":3},"title":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding.","author":"Henry Rzepa","date":"March 10, 2017","format":false,"excerpt":"A few years back, I did a post about the Pirkle reagent and the unusual \u03c0-facial hydrogen bonding structure it exhibits. For the Pirkle reagent, this bonding manifests as a close contact between the acidic OH hydrogen and the edge of a phenyl ring; the hydrogen bond is off-centre from\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\/2017\/03\/142-1024x770.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","url_meta":{"origin":18582,"position":4},"title":"\u03c0-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?","author":"Henry Rzepa","date":"April 15, 2017","format":false,"excerpt":"Back in the early 1990s, we first discovered the delights of searching crystal structures\u00a0for unusual\u00a0bonding features. One of the first cases was a search for hydrogen bonds formed to the\u00a0\u03c0-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it's\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\/2017\/04\/SQ-H-pi-1024x783.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":22231,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22231","url_meta":{"origin":18582,"position":5},"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":[]}],"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\/18582","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=18582"}],"version-history":[{"count":27,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18582\/revisions"}],"predecessor-version":[{"id":18618,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18582\/revisions\/18618"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18582"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18582"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18582"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18582"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}