{"id":1603,"date":"2010-01-31T11:01:32","date_gmt":"2010-01-31T10:01:32","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1603"},"modified":"2010-07-26T08:22:50","modified_gmt":"2010-07-26T07:22:50","slug":"the-conformational-analysis-of-cyclo-octane","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1603","title":{"rendered":"The conformational analysis of cyclo-octane"},"content":{"rendered":"
\n

In the previous post, I suggested that inspecting the imaginary modes of planar cyclohexane might be a fruitful and systematic way in which at least parts of the conformational surface of this ring might be probed. Here, the same process is conducted for cyclo-octane<\/strong>. The ring starts with planar D8h<\/sub> symmetry, and at this geometry (B3LYP\/6-311G(d,p), DOI: 10042\/to-3742<\/a>) five negative force constants (corresponding to imaginary modes) are calculated. The most negative is non-degenerate, and gives directly the crown conformation of D4d<\/sub> symmetry (DOI: 10042\/to-3738<\/a>). The remaining four modes comprise two degenerate pairs. Following either of the E2u<\/sub> eigenvectors downhill leads to another conformation, D2d<\/sub> (DOI: 10042\/to-3741<\/a>), with a geometry which is noteworthy for exhibiting a pair of unusually close non-bonded H…H contacts (1.908\u00c5). This value is about \u00a00.3\u00c5 shorter than the sum of the Wan der Waals radii (DOI:\u00a010.1021\/jp8111556<\/a>).\u00a0We can debate whether such a close approach or inter-penetration of two hydrogens is a bond or not (an AIM analysis appears at the bottom of this post).<\/p>\n\n\n\n\n\n\n\n
D8h, +82.8 kcal\/mol<\/th>\n<\/tr>\n
Follow B2u<\/sub> 467i<\/em><\/th>\nFollow E3g<\/sub> 404i<\/em><\/th>\nFollow E2u<\/sub> 230i<\/em><\/th>\n<\/tr>\n
to D4d<\/sub> +0.8<\/th>\nto Ci<\/sub> 131i<\/em> (Au<\/sub>), +7.5<\/th>\nto D2d<\/sub> +3.6<\/th>\n<\/tr>\n
\"\"

B2u<\/p><\/div><\/th>\n

\"\"

E3g<\/p><\/div><\/th>\n

\"\"

E2u<\/p><\/div><\/th>\n<\/tr>\n

Cs <\/sub>0.0<\/span><\/th>\nC2<\/sub> +1.6<\/th>\n–<\/th>\n<\/tr>\n<\/tbody>\n<\/table>\n

Following the remaining E3g<\/sub> mode leads to a stationary point of Ci<\/sub> symmetry (DOI: 10042\/to-3743<\/a>). This is a valley-ridge potential, since this point turns out to be a transition state itself, and following the Au<\/sub> imaginary mode at this point results in another, this time stable conformation, of chiral C2<\/sub> symmetry (DOI: 10042\/to-3744<\/a>). This has a calculated optical rotation [\u03b1]D<\/sub> of 72\u00b0 (at 589nm in chloroform).<\/p>\n

Are these three conformations all there are? Well, a thorough analysis of the conformational space has in fact identified six minima (DOI: 10.1002\/(SICI)1096-987X(19980415)19:5<524::AID-JCC5>3.0.CO;2-O<\/a>), of which the most stable has Cs<\/sub> symmetry (the so-called chair-boat<\/strong> conformation, and the one most frequently found in crystal structures of cyclo-octanes). Where is that one in the above analysis? It arrives by a distortion of the D4d<\/sub> form (DOI: 10042\/to-3747<\/a>) via<\/em> a transition state of no symmetry (DOI: 10042\/to-3752<\/a>)<\/p>\n

Whilst the full potential surface clearly has many more features, following the modes of the planar conformation of cyclo-octane is a simple and rapid way of establishing four of the six limiting stable conformations (the two remaining forms have \u00a0D2<\/sub> and S4<\/sub> symmetry, see DOI 10.1016\/0166-1280(88)80008-3<\/a>).<\/p>\n

\"\"<\/a>

AIM analysis of D2d cyclo-octane.<\/p><\/div>\n

Finally as promised, the AIM analysis of the D2d<\/sub> conformer (above). The \u03c1(r) value at the interesting H…H critical point is 0.015, which is pretty high in comparison to most normal hydrogen bonds, and would be conventionally taken to indicate attraction<\/strong>. The Laplacian \u22072<\/sup>\u03c1(r) is +0.05. The “bond” ellipticity \u03b5 has a value of 0.29. Single bonds are close to zero, and C=C double bonds are ~0.4, so this is pretty high (see also DOI:\u00a010.1002\/anie.200805751<\/a>).<\/p>\n

The two highest C-H stretching vibrations for this conformation are well separated from all the others (\u03bd 3095, 3103 cm-1<\/sup> for the symmetric A1<\/sub> and antisymmetric B2<\/sub> combinations, below for animations). These vibrations serve to both decrease and increase the H…H distances as part of the atomic (harmonic) displacements, and clearly doing so takes more energy than vibrating any of the other C-H bonds. It seems unlikely that the C-H bonds are themselves stronger, so does that mean that the H…H interaction is attractive or is it repulsive? In this context, it is worth noting that the symmetric vibration (both H…H distances decrease\/increase at the same time) is lower in wavenumber than the mode which decreases one and increases the other.<\/p>\n\n\n\n
\"\"

A1<\/p><\/div><\/td>\n

\"\"

B2<\/p><\/div><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

In the previous post, I suggested that inspecting the imaginary modes of planar cyclohexane might be a fruitful and systematic way in which at least parts of the conformational surface of this ring might be probed. Here, the same process is conducted for cyclo-octane. The ring starts with planar D8h symmetry, and at this geometry […]<\/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":[1],"tags":[183,17,268,24,2646],"ppma_author":[2661],"class_list":["post-1603","post","type-post","status-publish","format-standard","hentry","category-general","tag-3g","tag-conformational-analysis","tag-cuyclooctane","tag-energy","tag-general"],"yoast_head":"\nThe conformational analysis of cyclo-octane - 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=1603\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The conformational analysis of cyclo-octane - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In the previous post, I suggested that inspecting the imaginary modes of planar cyclohexane might be a fruitful and systematic way in which at least parts of the conformational surface of this ring might be probed. 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The method also gave interesting results for the larger cyclo-octane ring. How about a larger leap into the unknown? Let us proceed as follows. One fun\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\/02\/B3N3H12.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":1587,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1587","url_meta":{"origin":1603,"position":1},"title":"The conformation of cyclohexane","author":"Henry Rzepa","date":"January 28, 2010","format":false,"excerpt":"Like benzene, its fully saturated version cyclohexane represents an icon of organic chemistry. By 1890, the structure of planar benzene was pretty much understood, but organic chemistry was still struggling somewhat to fully embrace three rather than two dimensions. A grand-old-man of organic chemistry at the time, Adolf von Baeyer,\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"D6h to C2h for cyclohexane","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/01\/cx-c2h.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":1856,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1856","url_meta":{"origin":1603,"position":2},"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":21407,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21407","url_meta":{"origin":1603,"position":3},"title":"Does Kekulene have Kekul\u00e9 vibrational modes? Yes!","author":"Henry Rzepa","date":"October 19, 2019","format":false,"excerpt":"Increasingly, individual small molecules are having their structures imaged using STM, including cyclo[18]carbon that I recently discussed. The latest one receiving such treatment is Kekulene. As with cyclo[18]carbon, the point of interest was which of the two resonance structures shown below most closely resembled the measured structure. The one on\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\/10\/b3-1423-B2u-1024x575.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":7926,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7926","url_meta":{"origin":1603,"position":4},"title":"Ring-flipping in cyclohexane in a different light","author":"Henry Rzepa","date":"October 12, 2012","format":false,"excerpt":"The conformational analysis of cyclohexane is a mainstay of organic chemistry. Is there anything new that can be said about it? Let us start with the diagram below: This identifies the start of the process as a chair conformation of cyclohexane, with D3d symmetry. I have highlighted a pair of\u2026","rel":"","context":"In \"chair\"","block_context":{"text":"chair","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=chair"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/10\/37.svg","width":350,"height":200},"classes":[]},{"id":20679,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20679","url_meta":{"origin":1603,"position":5},"title":"Imaging vibrational normal modes of a single molecule.","author":"Henry Rzepa","date":"April 18, 2019","format":false,"excerpt":"The topic of this post originates from a recent article which is attracting much attention. The technique uses confined light to both increase the spatial resolution by around three orders of magnitude and also to amplify the signal from individual molecules to the point it can be recorded. To me,\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\/04\/Figure3a-1024x529.jpg?resize=350%2C200&ssl=1","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\/1603","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=1603"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/1603\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1603"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1603"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1603"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=1603"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}