{"id":5040,"date":"2011-10-10T15:37:54","date_gmt":"2011-10-10T15:37:54","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5040"},"modified":"2012-10-28T09:03:02","modified_gmt":"2012-10-28T09:03:02","slug":"are-close-h%e2%80%a6h-contacts-bonds-the-denouement","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5040","title":{"rendered":"Are close H\u2026H contacts bonds? The d\u00e9nouement!"},"content":{"rendered":"
\n

I wrote earlier<\/a> about the strangely close contact between two hydrogen atoms in cis<\/em>-butene. The topology of the electron density showed characteristics of a bond, but is it a consensual union? The two hydrogens approach closer than their van der Waals radii would suggest is normal, so something is happening, but that something need not be what chemists might choose to call a “bond<\/strong>“. An NCI (non-covalent analysis) hinted that any stability due to the electron topologic characteristics of a bond (the BCP) might be more than offset by the repulsive nature of the adjacent ring critical point (RCP). Here I offer an alternative explanation for why the two hydrogens approach so closely.<\/p>\n\n\n\n
\n
\"\"

One of four C-H NBO donor orbitals. Click for 3D<\/p><\/div>\n<\/td>\n

\n
\"\"

The empty C=C \u03c0* orbital. Click for 3D to show both orbitals superimposed.<\/p><\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

We need to try to “concentrate” or “focus” the effect into the bonds of the molecule, and a good way of doing this is to calculate the NBO (natural bond orbitals). The first we focus on is localised onto one (of four) C-H bonds of the methyl group; the other is the anti bonding\u00a0\u03c0* orbital of the alkene. NBO theory allows us to calculate how these two orbitals perturb each other, in the sense of the occupied orbital donating to the empty orbital. This energy is known as E(2), and for any of the four (equivalent) interactions above, it is computed at 5.17 kcal\/mol. If you look closely at the orbitals, the C-H bond is leaning away from the centre, but so is the \u03c0* acceptor orbital (that is the nature of anti bonding orbitals). These characteristics improve the overlap of the orbitals, and hence tend to increase the value of E(2).<\/p>\n

What about an alternative conformation of cis-butene in which the close contact of the H…H atoms is removed by rotation? Well, the C-H NBOs now rotate in, but the anti bonding\u00a0\u03c0* orbital still tilts out. The overlap between them is no longer quite so good, and indeed the E(2) energy decreases to 4.43 kcal\/mol.<\/p>\n\n\n\n
\n
\"\"

Donor C-H bond in rotated isomer of cis-butene. Click for \u00a03D<\/p><\/div>\n<\/td>\n

\n
\"\"

NBO C=C p* orbital in rotated isomer of cis-butene. Click for \u00a03D<\/p><\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

How many more orbitals should be considered? Well, the NBO technique in effect concentrates these effects into a relatively small number of orbitals (those separated by the smallest energy gap). We can also add in the four interactions between the bonding\u00a0\u03c0 orbital and the anti-bonding C-H* NBO. The totals for the first conformation come to 34.08 and for the second 30.44.<\/p>\n

So we can conclude by observing that cis<\/em>-butene makes a sacrifice for its greater good. Rotating the methyl groups means that the overlap of four C-H bonds with the alkene is optimised, but an undesired side effect is to induce two hydrogens to get close to each other. They would not normally be happy doing so, but the gain from the first effect is greater than the loss from the second. Whilst they may be close, chemists would prefer not to call the H-H approach a bond, even though the topology of the electron density might say it is.<\/p>\n

By the way, this is my 150th post. I had little idea when I started that I might reach this milestone.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

I wrote earlier about the strangely close contact between two hydrogen atoms in cis-butene. The topology of the electron density showed characteristics of a bond, but is it a consensual union? The two hydrogens approach closer than their van der Waals radii would suggest is normal, so something is happening, but that something need not […]<\/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":[1,4],"tags":[17,24,684,685,373],"ppma_author":[2661],"class_list":["post-5040","post","type-post","status-publish","format-standard","hentry","category-general","category-interesting-chemistry","tag-conformational-analysis","tag-energy","tag-energy-decreases","tag-smallest-energy-gap","tag-tutorial-material"],"yoast_head":"\nAre close H\u2026H contacts bonds? 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It was a very rare computed example of a system where the added two electrons populate the higher valence shells known as Rydberg orbitals as an alternative to populating the C-F antibonding \u03c3-orbital to produce CH3- and F-. The net\u2026","rel":"","context":"In "Hypervalency"","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":4987,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4987","url_meta":{"origin":5040,"position":1},"title":"Are close H…H contacts bonds?","author":"Henry Rzepa","date":"October 7, 2011","format":false,"excerpt":"The properties of electrons are studied by both chemists and physicists. At the boundaries of these two disciplines, sometimes interesting differences in interpretation emerge. One of the most controversial is that due to Bader (for a recent review, see DOI: 10.1021\/jp102748b) a physicist who brought the mathematical rigor of electronic\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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19207,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19207","url_meta":{"origin":5040,"position":2},"title":"Ammonide: an alkalide formed from ammonia and resembling an electride.","author":"Henry Rzepa","date":"December 17, 2017","format":false,"excerpt":"Alkalides are anionic alkali compounds containing e.g.\u00a0sodide (Na-), kalide (K-), rubidide (Rb-) or caeside (Cs-). Around 90 examples can be found in the Cambridge structure database (see DOI: 10.14469\/hpc\/3453\u00a0 for the search query and results). So what about the ammonium analogue, ammonide (NH4-)? A quick search of Scifinder drew a\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\/2017\/12\/A1.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":1856,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1856","url_meta":{"origin":5040,"position":3},"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":24452,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24452","url_meta":{"origin":5040,"position":4},"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":22471,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22471","url_meta":{"origin":5040,"position":5},"title":"Fascinating stereoelectronic control in Metaldehyde and Chloral.","author":"Henry Rzepa","date":"June 9, 2020","format":false,"excerpt":"Metaldehyde is an insecticide used to control slugs. When we unsuccessfully tried to get some recently, I discovered it is now deprecated in the UK. So my immediate reaction was to look up its structure to see if that cast any light (below, R=CH3, shown as one stereoisomer). A X-ray\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\/5040","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=5040"}],"version-history":[{"count":4,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5040\/revisions"}],"predecessor-version":[{"id":8113,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5040\/revisions\/8113"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5040"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5040"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5040"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=5040"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}