{"id":17089,"date":"2016-11-14T17:21:26","date_gmt":"2016-11-14T17:21:26","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17089"},"modified":"2016-12-03T10:18:26","modified_gmt":"2016-12-03T10:18:26","slug":"hydrogen-bonding-to-chloroform","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089","title":{"rendered":"Hydrogen bonding to chloroform."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"17089\">\n<p>Chloroform, often in the deuterated form CDCl<sub>3<\/sub>, 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 molecules. But what are the features of the hydrogen bonds that form from chloroform to other acceptors? Here I do a quick search for the common characteristics of such interactions.<\/p>\n<ol>\n<li>This first search (R &lt; 0.05, no errors, no disorder) is for interactions from the CH&#8230; O, and is a plot of that distance against the angle subtended at the oxygen.\n<p><img decoding=\"async\" class=\"aligncenter size-full wp-image-17090\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-rt.jpg\" alt=\"clcho-rt\" width=\"450\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-rt.jpg 725w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-rt-300x201.jpg 300w\" sizes=\"(max-width: 725px) 100vw, 725px\" \/><\/p>\n<p>Note that there are not that many crystalline examples. The &#8220;hotspot&#8221; is at a distance of ~2.3\u00c5, but real examples down to 1.9\u00c5 exist. The angle subtended at the oxygen is close to 120\u00b0 (the angle subtended at the hydrogen is always close to 180\u00b0). The plot below constrains the search to data collected below 140K to reduce the thermal noise in the measurements, with the hotspot shortening slightly to 2.2\u00c5.\u00a0<img decoding=\"async\" class=\"aligncenter size-full wp-image-17091\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-140.jpg\" alt=\"clcho-140\" width=\"450\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-140.jpg 723w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-140-300x213.jpg 300w\" sizes=\"(max-width: 723px) 100vw, 723px\" \/><\/p>\n<\/li>\n<li>The next search is for interactions to N rather than O (T &lt; 140K). There are rather fewer hits, but again with similar features.<img decoding=\"async\" class=\"aligncenter size-full wp-image-17094\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHN-140.jpg\" alt=\"clchn-140\" width=\"450\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHN-140.jpg 719w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHN-140-300x187.jpg 300w\" sizes=\"(max-width: 719px) 100vw, 719px\" \/><\/li>\n<li>Finally, an attempt to see if there is a correlation between the C-H length and the H&#8230;O length.\u00a0<img decoding=\"async\" class=\"aligncenter size-full wp-image-17095\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/CH-vs-CO.jpg\" alt=\"ch-vs-co\" width=\"450\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/CH-vs-CO.jpg 723w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/CH-vs-CO-300x218.jpg 300w\" sizes=\"(max-width: 723px) 100vw, 723px\" \/>\n<p>This has odd characteristics, which suggests that in most cases the C-H distance is not measured from the diffraction data but simply &#8220;idealised&#8221; (and which therefore renders this plot meaningless). Unless its been added recently, it is not possible to specify in the search how the hydrogen positions have been refined, if at all and hence to restrict the search only to those structures where the C-H distance is meaningful.<\/p>\n<\/li>\n<\/ol>\n<p>In the last ten years or so, great progress has been made in assigning experimental spectra with the help of quantum calculations. This is true of chemical shifts in NMR, but especially so for chiroptical measurements such as ORP, ECD and VCD. Given that explicit hydrogen bonds can introduce anisotropy into the otherwise isotropic solvent continuum, it might be worth including perhaps one chloroform molecule into these calculations, especially if the \u00a0CH&#8230;O distance is &lt;2\u00c5 (which suggests it is fairly strong). If nothing else, chloroform is rather big and might exert effects based on dispersion attractions or steric repulsions as well as the H-bonding.<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 17089 -->","protected":false},"excerpt":{"rendered":"<p>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 molecules. But what are the [&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":true,"_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":[49,1912,1911,1913,1449,1705,33],"ppma_author":[2661],"class_list":["post-17089","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-chemical-shifts","tag-chloroform","tag-deuterated-chloroform","tag-deuterated-methanol","tag-hydrogen-bond","tag-nuclear-magnetic-resonance","tag-spectroscopy"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Hydrogen bonding to chloroform. - 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=17089\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Hydrogen bonding to chloroform. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"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 molecules. But what are the [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-11-14T17:21:26+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-12-03T10:18:26+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-rt.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":"Hydrogen bonding to chloroform. - 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=17089","og_locale":"en_GB","og_type":"article","og_title":"Hydrogen bonding to chloroform. - Henry Rzepa&#039;s Blog","og_description":"Chloroform, often in the deuterated form CDCl3, is a very common solvent for NMR and other types of spectroscopy. 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But what are the [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2016-11-14T17:21:26+00:00","article_modified_time":"2016-12-03T10:18:26+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-rt.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=17089#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Hydrogen bonding to chloroform.","datePublished":"2016-11-14T17:21:26+00:00","dateModified":"2016-12-03T10:18:26+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089"},"wordCount":399,"commentCount":5,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/ClCHO-rt.jpg","keywords":["chemical shifts","Chloroform","Deuterated chloroform","Deuterated methanol","Hydrogen bond","Nuclear magnetic resonance","spectroscopy"],"articleSection":["crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089","name":"Hydrogen bonding to chloroform. - 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