{"id":2207,"date":"2010-07-11T09:31:57","date_gmt":"2010-07-11T08:31:57","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207"},"modified":"2010-07-26T08:20:43","modified_gmt":"2010-07-26T07:20:43","slug":"tunable-bonds-looked-at-in-a-different-way","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207","title":{"rendered":"Tunable bonds looked at in a different way"},"content":{"rendered":"
\n

The title of this post merges those of the two previous<\/a> ones. The tunable C-Cl bond brought about in the molecule tris(amino)chloromethane by anomeric effects will be probed using the Laplacian of the electronic density<\/a>.<\/p>\n

\"\"

Laplacian @0.67 for tris(amino)choromethane. Click for 3D<\/p><\/div>\n

The figure above shows the Laplacian for a conformation of tris(amino)chloromethane with one of the nitrogen lone pairs antiperiplanar to the C-Cl bond, and the other two lone pairs antiperiplanar to C-N bonds. The features visible at an isosurface of \u00b1 0.67 include<\/p>\n

    \n
  1. (a) The Laplacian here has a value of -0.67 (= red isosurface), which indicates an accumulation of (covalent) shared density along the C-N bond (underneath this surface, you can see the blue sphere representing depletions from the nitrogen atomic region). This bond has the lone pair antiperiplanar to a C-N bond.<\/li>\n
  2. (b) Contrast this with the C-N bond which is antiperiplanar to the C-Cl bond. A greater volume of the covalent C-N region is bounded by this isosurface. More of the N lone pair on this atom is donating into the C-N, as more conventionally represented below.<\/li>\n
  3. Notice how the red isosurface associated with the N lone pair and the region associated with the C-N bond are in fact contiguous, and not separated basins!\n

  4. (c) represents the lone pairs on the chlorine, which have been augmented by the donation from the nitrogen. Notice how they come out as a torus rather than the conventional double dot representations!<\/li>\n
  5. Notice the absence of any features along the C-Cl bond! This would be typical of a fully or even partially ionic bond, but it also illustrates that with a property such as the Laplacian, one does not get a complete picture by inspecting at just one isosurface value.<\/li>\n<\/ol>\n

    The next isosurface chosen is 0.3. At this lower value, more depletions (blue = electrophilic regions) are seen and a tiny feature now appears along the C-Cl bond, which is the covalent accumulation of that bond, a feature that grows @ 0.2. This nicely illustrates the variable covalency\/ionicity of the C-Cl bond. Notice also how the lhs is all red (anionic) and the rhs is mostly blue (cationic), showing the formation of in effect an ion pair.<\/p>\n\n\n\n
    \n

    \"\"

    tris(amino)chloroethane @ 0.3<\/p><\/div><\/td>\n

    		\n

    \"\"

    tris(amino)chloroethane @ 0.2<\/p><\/div><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    There are many other features which can be explored in these Laplacian maps, but I leave those for the reader to indulge in. Just click on any of the diagrams above,and start your exploration.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    The title of this post merges those of the two previous ones. The tunable C-Cl bond brought about in the molecule tris(amino)chloromethane by anomeric effects will be probed using the Laplacian of the electronic density. The figure above shows the Laplacian for a conformation of tris(amino)chloromethane with one of the nitrogen lone pairs antiperiplanar to […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[260,262,2648,261],"ppma_author":[2661],"class_list":["post-2207","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-anomeric-effect","tag-chemical-energy","tag-interesting-chemistry","tag-laplacian"],"yoast_head":"\nTunable bonds looked at in a different way - 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=2207\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tunable bonds looked at in a different way - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The title of this post merges those of the two previous ones. The tunable C-Cl bond brought about in the molecule tris(amino)chloromethane by anomeric effects will be probed using the Laplacian of the electronic density. The figure above shows the Laplacian for a conformation of tris(amino)chloromethane with one of the nitrogen lone pairs antiperiplanar to […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2010-07-11T08:31:57+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2010-07-26T07:20:43+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/app-1-0.67.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":"Tunable bonds looked at in a different way - 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=2207","og_locale":"en_GB","og_type":"article","og_title":"Tunable bonds looked at in a different way - Henry Rzepa's Blog","og_description":"The title of this post merges those of the two previous ones. The tunable C-Cl bond brought about in the molecule tris(amino)chloromethane by anomeric effects will be probed using the Laplacian of the electronic density. The figure above shows the Laplacian for a conformation of tris(amino)chloromethane with one of the nitrogen lone pairs antiperiplanar to […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207","og_site_name":"Henry Rzepa's Blog","article_published_time":"2010-07-11T08:31:57+00:00","article_modified_time":"2010-07-26T07:20:43+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/app-1-0.67.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=2207#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Tunable bonds looked at in a different way","datePublished":"2010-07-11T08:31:57+00:00","dateModified":"2010-07-26T07:20:43+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207"},"wordCount":449,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/app-1-0.67.jpg","keywords":["Anomeric effect","Chemical Energy","Interesting chemistry","Laplacian"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207","name":"Tunable bonds looked at in a different way - 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=2207#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/app-1-0.67.jpg","datePublished":"2010-07-11T08:31:57+00:00","dateModified":"2010-07-26T07:20:43+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=2207#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207#primaryimage","url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/app-1-0.67.jpg","contentUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/app-1-0.67.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2207#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"Tunable bonds looked at in a different way"}]},{"@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-zB","jetpack-related-posts":[{"id":2183,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2183","url_meta":{"origin":2207,"position":0},"title":"Looking at bonds in a different way: the Laplacian.","author":"Henry Rzepa","date":"July 6, 2010","format":false,"excerpt":"The Cheshire cat in Alice's Adventures in Wonderland comes and goes at will, and engages Alice with baffling philosophical points. Chemical bonds are a bit like that too. In the previous post, we saw how (some) bonds can be tuned to be strong or weak simply by how a lone\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\/07\/ethane-0.3.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":2251,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2251","url_meta":{"origin":2207,"position":1},"title":"The weirdest bond of all? Laplacian isosurfaces for [1.1.1]Propellane.","author":"Henry Rzepa","date":"July 21, 2010","format":false,"excerpt":"In this post, I will take a look at what must be the most extraordinary small molecule ever made (especially given that it is merely a hydrocarbon). Its peculiarity is the region indicated by the dashed line below. Is it a bond? If so, what kind, given that it would\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/propellane.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":27944,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27944","url_meta":{"origin":2207,"position":2},"title":"A one-electron bond in methyl-\u03bb1-borane.","author":"Henry Rzepa","date":"October 9, 2024","format":false,"excerpt":"In exploring one-electron carbon-carbon bonds, I had noted previously that both hexafluoroethane and ethane itself could each lose an electron to produce such species. A discussion developed in which a molecule isoelectronic with ethane radical cation, namely the methyl-\u03bb1-borane radical (H3B-CH3) was proposed by Jacob. The optimised structure at the\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":27870,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27870","url_meta":{"origin":2207,"position":3},"title":"The one-electron carbon-carbon bond: Hexafluoroethane and ethane radical cations.","author":"Henry Rzepa","date":"October 3, 2024","format":false,"excerpt":"In the previous post, I looked at the recently reported hexa-arylethane containing a carbon-carbon one-electron bond, its structure having been determined by x-ray diffraction (XRD). The measured C-C bond length was ~2.9a\u00c5 and my conclusion was that the C...C region represented more of a weak \"interaction\" than of a bond\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":15608,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15608","url_meta":{"origin":2207,"position":4},"title":"Quintuple bonds: resurfaced.","author":"Henry Rzepa","date":"January 31, 2016","format":false,"excerpt":"Six years ago, I posted on the nature of a then recently reported Cr-Cr quintuple bond. The topic resurfaced as part of the discussion on a more recent post on NSF3, and a\u00a0sub-topic on\u00a0the nature of the higher order bonding in C2. The comment made a connection between that discussion\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/02\/Cr.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":27788,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27788","url_meta":{"origin":2207,"position":5},"title":"A carbon-carbon one-electron bond! Or a weak carbon-carbon interaction?","author":"Henry Rzepa","date":"October 1, 2024","format":false,"excerpt":"More than 100 years ago, before the quantum mechanical treatment of molecules had been formulated, G. N. Lewis proposed a simple model for chemical bonding that is still taught today. This is the idea of the three categories of bond we know as single, double and triple, comprising respectively two,\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":[]}],"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\/2207","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=2207"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2207\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2207"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2207"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2207"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=2207"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}