{"id":21096,"date":"2019-07-19T11:00:47","date_gmt":"2019-07-19T10:00:47","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21096"},"modified":"2019-07-19T11:33:31","modified_gmt":"2019-07-19T10:33:31","slug":"ch-o-hydrogen-bonding-competing-with-layered-dispersion-attractions","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21096","title":{"rendered":"CH…O hydrogen bonding competing with layered dispersion attractions."},"content":{"rendered":"
\n

I have previously<\/a> 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<\/strong> (DOI: 10.5517\/cc5fgpq<\/a>) identified from the searches appended to this post as interesting for further inspection.[1]<\/a><\/span><\/p>\n

\"\"<\/a><\/p>\n

The distances from the carbonyl oxygen to CH groups of an adjacent intermolecular molecule are shown, revealing a bifurcated strong + weaker CH…O interaction. I would note that the CH…O distances are un-normalized, in the sense that a C-H distance obtained from X-ray diffraction data is normally about 0.1\u00c5 too short. A corrected value for the H…O distance is probably closer to 1.994\u00c5. Next, a B3LYP+G3BJ\/Def2-TZVPP calculation of just this dimeric interaction, which shows a somewhat different pattern, particularly from the carbonyl to the sp3<\/sup>-C-H (FAIR data DOI: 10.14469\/hpc\/5943<\/a>) with one distance being shorter and one longer.<\/p>\n

\"\"<\/a>

Click to load 3D model<\/p><\/div>\n

A QTAIM analysis reveals the electron density\u00a0\u03c1(r) of 0.021au, a relatively high value indicating a relatively strong interaction.<\/p>\n

\"\"<\/a><\/p>\n

Side-views reveals a possible reason for why the calculation does not match the crystal structure. In the crystal structure, the sp3<\/sup>-CH2<\/sub> group adopts a different conformation from that computed for just two interacting molecules, since this shape allows more efficient stacking of layers and hence allowing stabilizing dispersion energy between the layers to overcome some loss of hydrogen bonding energies in the plane of the layer. If this packing constraint is removed in the pure dimer, one sp3<\/sup>-CH moves into the plane allowing a shorter interaction to the carbonyl oxygen and the other sp3<\/sup>-CH adopts a pure axial position, unconstrained by any packed layer above it.The absence of layered dispersion attractions is hence compensated by forming strong CH…O interactions.\"\"<\/a> \"\"<\/a><\/p>\n

A calculation using six molecules arranged in three layers of two is an attempt to add back at least some of the layering dispersion terms (a full periodic boundary lattice calculation is the proper way of doing this calculation, but at the level chosen here would take far too much computer time!). The new CH…O distances are now 2.018 and 2.384\u00c5 (compared to 2.036 and 2.199\u00c5 for a model with just two molecules). Probably, more layers would be needed to replicate the crystal structure more accurately.<\/p>\n

\"\"<\/p>\n

\n

And now for the searches. The first is for sp-hybridised carbon, as an intermolecular interaction (R < 0.05, no errors, no disorder, T=<150K, H-position normalised for distances shorter than the sum of the vdW radii -0.4), for which a clear hot spot occurs at a H…O distance of ~2.1\u00c5<\/p>\n

\"\"<\/a>

Intermolecular to sp carbon<\/p><\/div>\n

Next, sp2<\/sup>-C as an intermolecular interaction (T=<90K), where the hot spot is less distinct, being at the distance cut-off specified for the search. The shortest distance is ~2.0\u00c5. I will return to this example shortly.<\/p>\n

\"\"<\/a>

Intermolecular to sp2 carbon<\/p><\/div>\n

An intramolecular version of this search shows a clearer hotspot, again at ~2.15\u00c5<\/p>\n

\"\"<\/a>

Intramolecular to sp2 carbon<\/p><\/div>\n

Next, intramolecular sp3<\/sup> hybridisation, for which there few examples with no clear hotspot.<\/p>\n

\"\"<\/a>

Intramolecular to sp3 carbon<\/p><\/div>\n

Finally, intermolecular sp3<\/sup> hybridisation. The H…O distance hotspot is very slightly longer, as might be expected for a less acidic hydrogen. Nonetheless, the variation in the H…O distances with hybridisation is perhaps unexpectedly small.<\/p>\n

\"\"<\/a><\/p>\n

\n

To summarise, by performing a general search of the crystal structure database, one can identify general trends and then go to inspect outliers. In this case, this brought the focus onto an (dare I say otherwise umremarkable) molecule in which layers of aromatic molecules set up a competition between intra-layer CH…O hydrogen bonding and inter-layer dispersion stabilizations. I suspect this competition between these two type of weak interactions is far more common than is generally recognised.<\/p>\n

 <\/p>\n

References<\/h2>\n
  1. K.S. Huang, M.J. Haddadin, M.M. Olmstead, and M.J. Kurth, \"Synthesis and Reactions of Some Heterocyclic Azacyanines<sup>1<\/sup>\", The Journal of Organic Chemistry<\/i>, vol. 66, pp. 1310-1315, 2001. https:\/\/doi.org\/10.1021\/jo001484k<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    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 the searches appended to this […]<\/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-21096","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining"],"yoast_head":"\nCH...O hydrogen bonding competing with layered dispersion attractions. - 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=21096\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"CH...O hydrogen bonding competing with layered dispersion attractions. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 the searches appended to this […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21096\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2019-07-19T10:00:47+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2019-07-19T10:33:31+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/07\/XEVJIR-1024x839.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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"CH...O hydrogen bonding competing with layered dispersion attractions. - 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I occasionally comment with some aspect of one of the molecules that catches my eye (I have already written about cyclo[18]carbon, another in the list). Here, it is the Incredible chloride cage, a cryptand-like container with 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\/2019\/12\/cryptand-1024x847.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":17579,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","url_meta":{"origin":21096,"position":1},"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":18399,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18399","url_meta":{"origin":21096,"position":2},"title":"CH\u22c5\u22c5\u22c5\u03c0 Interactions between methyl and carbonyl groups in proteins: a small molecule check.","author":"Henry Rzepa","date":"May 29, 2017","format":false,"excerpt":"Derek Lowe highlights a recent article postulating\u00a0CH\u22c5\u22c5\u22c5\u03c0 interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD). The search query (DOI:\u00a010.14469\/hpc\/2594)\u00a0is shown below. The distance refers to that between the (normalised) position of a hydrogen on a 4-coordinated carbon atom and the centroid\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\/05\/152-1024x637.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24452,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24452","url_meta":{"origin":21096,"position":3},"title":"Biotin\u2019s biggest lesson is the importance of nonclassical H-bonds in protein\u2212ligand complexes.","author":"Henry Rzepa","date":"November 27, 2021","format":false,"excerpt":"The title comes from the abstract of an article analysing why Biotin (vitamin B7) is such a strong and effective binder to proteins, with a free energy of (non-covalent) binding approaching 21 kcal\/mol. The author argues that an accumulation of both CH-\u03c0 and CH-O together with more classical hydrogen bonds\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":24483,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24483","url_meta":{"origin":21096,"position":4},"title":"Protein-Biotin complexes. Crystal structure mining.","author":"Henry Rzepa","date":"December 12, 2021","format":false,"excerpt":"In the previous post, I showed some of the diverse \"non-classical\"interactions between Biotin and a protein where it binds very strongly. Here I take a look at two of these interactions to discover how common they are in small molecule structures. The first search is of a CH hydrogen bond\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\/2021\/12\/Screenshot-983-1024x893.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":17089,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089","url_meta":{"origin":21096,"position":5},"title":"Hydrogen bonding to chloroform.","author":"Henry Rzepa","date":"November 14, 2016","format":false,"excerpt":"Chloroform, often in the deuterated form CDCl3, is a very common solvent for NMR and other types of spectroscopy. Quantum mechanics\u00a0is increasingly used to calculate such spectra to aid assignment and the solvent is here normally simulated as a continuum rather than by explicit inclusion of one or more chloroform\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":[]}],"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\/21096","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=21096"}],"version-history":[{"count":18,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21096\/revisions"}],"predecessor-version":[{"id":21127,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21096\/revisions\/21127"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21096"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21096"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21096"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21096"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}