{"id":2144,"date":"2010-07-03T09:28:29","date_gmt":"2010-07-03T08:28:29","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2144"},"modified":"2010-07-11T11:56:13","modified_gmt":"2010-07-11T10:56:13","slug":"tunable-bonds","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2144","title":{"rendered":"Tunable bonds"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"2144\">\n<p>Car transmissions come in two types, ones with fixed ratio gears, and ones which are continuously variable. When it comes to chemical bonds, we tend to think of them as being very much of the first type. Bonds come in fixed ratios; single, aromatic, double, triple, etc. OK, they do vary, but the variations are assumed as small perturbations on the basic form. Take for example the molecule shown below. The bonds as shown are all clearly single (the wedge and hashed bond are merely stereochemical notations). No-one would really think of drawing this molecule in any other way, and this idea of the transferability of bonds between molecules (all double bonds react in specific ways which are different from single bonds, and they also have characteristic spectroscopic properties, etc) is what allows molecules to be classified.<\/p>\n<div id=\"attachment_2145\" style=\"width: 178px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/ultimate_anomeric.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2145\" class=\"size-full wp-image-2145\" title=\"A Highly tunable molecule\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/ultimate_anomeric.jpg\" alt=\"\" width=\"168\" height=\"125\" \/><\/a><p id=\"caption-attachment-2145\" class=\"wp-caption-text\">A Highly tunable molecule<\/p><\/div>\n<p>With this molecule however, there really is an elephant in the room; the three electron lone pairs associated with each nitrogen atom (not shown above, but most chemists are trained to recognize their implicit presence). Where are they? Well, each lone pair will tend to orient itself such that it is aligned with an adjacent \u03c3-bond. It has two such bonds to choose from, an adjacent C-N bond or a C-Cl bond.  One might now envisage the following permuations; all three N lone pairs <em>gang-up<\/em> on the C-Cl bond, or perhaps only two do, or only one, or none. What happens in each of these scenarios? The table below shows these permutations calculated using B3LYP\/6-31G(d).<\/p>\n<table border=\"1\">\n<tbody>\n<tr>\n<th>app\u00a0lone pairs<br \/>\nto C-Cl<\/th>\n<th>Relative free<br \/>\nenergy, kcal\/mol<\/th>\n<th>C-Cl bond<br \/>\nlength, \u00c5<\/th>\n<th>\u03bd C-Cl, cm<sup>-1<\/sup><\/th>\n<\/tr>\n<tr>\n<td>3<\/td>\n<td>0.0<\/td>\n<td>2.542<\/td>\n<td>158<\/td>\n<\/tr>\n<tr>\n<td>2<\/td>\n<td>4.2<\/td>\n<td>2.099<\/td>\n<td>221<\/td>\n<\/tr>\n<tr>\n<td>1<\/td>\n<td>7.3<\/td>\n<td>1.937<\/td>\n<td>352<\/td>\n<\/tr>\n<tr>\n<td>0<\/td>\n<td>14.4<\/td>\n<td>1.869<\/td>\n<td>441<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<table border=\"0\">\n<tbody>\n<tr>\n<td>\n<p><div id=\"attachment_2148\" style=\"width: 113px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2148\" class=\"size-full wp-image-2148\" title=\"3 app lone pairs\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('green');jmolApplet([600,600],'load wp-content\/uploads\/2010\/07\/anomeric_3.log;frame 33;set measurementUnits Angstroms;delay 5;vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 15;animation mode loop;connect (atomno=1) (atomno=11) PARTIAL;measure 1 11;set fontscaling TRUE;font label 36;select atomno=11;label %A 158 cm-1;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/anomeric-3.jpg\" alt=\"\" width=\"103\" height=\"106\" \/><p id=\"caption-attachment-2148\" class=\"wp-caption-text\">3 app lone pairs. Click for animation<\/p><\/div><\/td>\n<td>\n<p><div id=\"attachment_2149\" style=\"width: 113px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2149\" class=\"size-full wp-image-2149\" title=\"2 app lone pairs\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('yellow');jmolApplet([600,600],'load wp-content\/uploads\/2010\/07\/anomeric_2.log;frame 24;set measurementUnits Angstroms;delay 5;vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 15;animation mode loop;connect (atomno=1) (atomno=11) PARTIAL;measure 1 11;set fontscaling TRUE;font label 36;select atomno=11;label %A 221 cm-1;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/anomeric-2.jpg\" alt=\"\" width=\"103\" height=\"106\" \/><p id=\"caption-attachment-2149\" class=\"wp-caption-text\">2 app lone pairs. Click for animation<\/p><\/div><\/td>\n<\/tr>\n<tr>\n<td>\n<p><div id=\"attachment_2150\" style=\"width: 113px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2150\" class=\"size-full wp-image-2150\" title=\"1 app lone pairs\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('red');jmolApplet([600,600],'load wp-content\/uploads\/2010\/07\/anomeric_1.log;frame 36;set measurementUnits Angstroms;delay 5;vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 15;animation mode loop;connect (atomno=1) (atomno=11) PARTIAL;measure 1 11;set fontscaling TRUE;font label 36;select atomno=11;label %A 352 cm-1;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/anomeric-1.jpg\" alt=\"\" width=\"103\" height=\"106\" \/><p id=\"caption-attachment-2150\" class=\"wp-caption-text\">1 app lone pairs. Click for animation<\/p><\/div><\/td>\n<td>\n<p><div id=\"attachment_2151\" style=\"width: 113px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2151\" class=\"size-full wp-image-2151\" title=\"0 app lone pairs\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('blue');jmolApplet([600,600],'load wp-content\/uploads\/2010\/07\/anomeric_0.log;frame 32;set measurementUnits Angstroms;delay 5;vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 15;animation mode loop;connect (atomno=1) (atomno=11) PARTIAL;measure 1 11;set fontscaling TRUE;font label 36;select atomno=11;label %A 441 cm-1;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/anomeric-0.jpg\" alt=\"\" width=\"103\" height=\"106\" \/><p id=\"caption-attachment-2151\" class=\"wp-caption-text\">0 app lone pairs. Click for animation<\/p><\/div><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>The C-Cl bond length changes from a <em>normal<\/em> single bond length (1.87\u00c5) when none of the nitrogen lone pairs are antiperiplanar to the C-Cl bond, to a very <em>abnormal<\/em> 2.54\u00c5 when all three are, and the C-Cl stretching mode decreases in wavenumber from 441 to 158 cm<sup>-1<\/sup>. There is lots of other fun to be had inspecting the geometries and vibrations, but \u00a0I will leave that for you to explore rather than discuss it here. Click on the thumbnails above to start.<\/p>\n<p>This effect does have a name, sugar chemists call it the <em>anomeric effect<\/em>. But this one is supercharged! It would be quite reasonable to say that at some stage, the C-Cl single bond turns from being covalent to being ionic (and indeed, repeating the calculation using an applied solvent field certainly accelerates this process). Whilst this might be a contrived example and hence an extreme example, it does serve to remind us that on occasion, molecules may come with continuously variable transmissions rather than with fixed ratio gears!<\/p>\n<p>And a postscript. I mentioned the nitrogen lone pairs ganging up on the  C-Cl bond.  How might one go even one step further?  A standard trick to enhance the donating power of a nitrogen lone pair is to replace the  NH<sub>2<\/sub> group with a hydrazine group,  H<sub>2<\/sub>N-NH.  The lone pair derived from the second nitrogen buttresses the first. This too has a name, it is called the  \u03b1-effect.<\/p>\n<div id=\"attachment_2166\" style=\"width: 207px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/hydrzine_ultimate_anomeric.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2166\" class=\"size-full wp-image-2166\" title=\"An anomeric effect on steroids\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/hydrzine_ultimate_anomeric.jpg\" alt=\"\" width=\"197\" height=\"125\" \/><\/a><p id=\"caption-attachment-2166\" class=\"wp-caption-text\">An anomeric effect on steroids<\/p><\/div>\n<p>For this example  (see <a href=\"http:\/\/hdl.handle.net\/10042\/to-5008\" target=\"_blank\">digital repository<\/a>), the C-Cl bond length lengthens even further to  2.90\u00c5, which interestingly, is the same value as for the <a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1135\" target=\"_blank\">SN1 transition state<\/a>!<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 2144 -->","protected":false},"excerpt":{"rendered":"<p>Car transmissions come in two types, ones with fixed ratio gears, and ones which are continuously variable. When it comes to chemical bonds, we tend to think of them as being very much of the first type. Bonds come in fixed ratios; single, aromatic, double, triple, etc. OK, they do vary, but the variations are [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_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},"jetpack_post_was_ever_published":false},"categories":[4],"tags":[152,146,40,242,241,2648],"ppma_author":[2661],"class_list":["post-2144","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-animation","tag-chemical-bonds","tag-free-energy","tag-h-2-n-nh","tag-hydrazine","tag-interesting-chemistry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.6 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Tunable bonds - 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=2144\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tunable bonds - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Car transmissions come in two types, ones with fixed ratio gears, and ones which are continuously variable. 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The query restricts the search to each carbon having just two non-metallic substituents. To avoid conjugation with these, they each are 4-coordinated; the carbons themselves are three-coordinated. Further constraints are the usual\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"sq","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/12\/sq-1024x415.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19102,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19102","url_meta":{"origin":2144,"position":1},"title":"Hypervalence and octet-expansion in trimethylene-\u03bb6-sulfane and related species.","author":"Henry Rzepa","date":"November 27, 2017","format":false,"excerpt":"Previously: \"Non-polar\" species such as SeMe6, SMe6, ClMe3, ClMe5 all revealed interesting properties for the Se-C, S-C or Cl-C \"single\" bonds. The latter two examples in particular hinted at internal structures for these single bonds, as manifested by two ELF basins for some of the bonds. Here I take a\u2026","rel":"","context":"In &quot;Hypervalency&quot;","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":5441,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5441","url_meta":{"origin":2144,"position":2},"title":"Driving the smallest car ever made: a chemical perspective.","author":"Henry Rzepa","date":"November 10, 2011","format":false,"excerpt":"Fascination with nano-objects, molecules which resemble every day devices, is increasing. Thus the world's smallest car has just been built. The mechanics of such a device can often be understood in terms of chemical concepts taught to most students. So I thought I would have a go at this one!\u2026","rel":"","context":"In &quot;General&quot;","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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/11\/car1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":5345,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5345","url_meta":{"origin":2144,"position":3},"title":"Atropisomerism in Taxol. An apparently simple bond rotation?","author":"Henry Rzepa","date":"November 1, 2011","format":false,"excerpt":"My previous post introduced the interesting guts of taxol. Two different isomers can exist, and these are called atropisomers; one has the carbonyl group pointing up, the other down. The barrier to their interconversion in this case is generated by a rotation about the two single bonds connecting the carbonyl\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/11\/taxol2.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17168,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17168","url_meta":{"origin":2144,"position":4},"title":"Molecule of the year? &#8220;CrN123&#8221;, a molecule with three different types of Cr-N bond.","author":"Henry Rzepa","date":"December 16, 2016","format":false,"excerpt":"Here is a third candidate for the C&EN \"molecule of the year\" vote. This one was shortlisted because it is the first example of a metal-nitrogen complex exhibiting single, double and triple bonds from different nitrogens to the same metal (XUZLUB has a 3D display available at DOI: 10.5517\/CC1JYY6M). Since\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","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":17115,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17115","url_meta":{"origin":2144,"position":5},"title":"Long C-C bonds.","author":"Henry Rzepa","date":"November 30, 2016","format":false,"excerpt":"In an earlier post, I searched for small C-C-C angles, finding one example that was also accompanied by an apparently exceptionally long C-C bond (2.18\u00c5). But this arose from highly unusual bonding giving rise not to a single bond order but one closer to one half! How long can a\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"long-cc","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/11\/long-cc-1024x757.jpg?resize=350%2C200","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\/2144","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=2144"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2144\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2144"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2144"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2144"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=2144"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}