{"id":12204,"date":"2014-03-29T15:35:03","date_gmt":"2014-03-29T15:35:03","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=12204"},"modified":"2014-03-31T17:12:50","modified_gmt":"2014-03-31T16:12:50","slug":"modelling-the-geometry-of-unbranched-alkanes","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12204","title":{"rendered":"Modelling the geometry of unbranched alkanes."},"content":{"rendered":"
\n

By about C17<\/sub>H36<\/sub>, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations. [1]<\/a><\/span> Indeed, a (co-crystal) of C16<\/sub>H34<\/sub> shows it to have two-gauche bends.[2]<\/a><\/span>.\u00a0Surprisingly, the longest linear alkane I was able to find a crystal structure for, C28<\/sub>H58<\/sub>\u00a0appears to be fully extended[3]<\/a><\/span>,[4]<\/a><\/span> (an early report of a low quality structure for C36<\/sub>H74<\/sub>[5]<\/a><\/span> also appears to show it as linear).\u2021<\/sup> Here I explore how standard DFT theories cope with these structures.<\/p>\n

I start with noting the use of a TZVP basis set. In a recent article[6]<\/a><\/span> we noted that the basis-set-superposition-errors for this basis were about a quarter of that for the standard Pople-type 6-311G(d,p) basis that I tend to use for modelling in this blog. This matters, since the relative energy of a folded-conformation vs<\/em> an extended linear one might depend on the quality of the basis set and its inherent BSSE. The DFT method is the classical B3LYP. I also modelled C58<\/sub>H118<\/sub> as the hydrocarbon as being well beyond the region anticipated above for folding of the chain to have started (no, there is no crystal structure). The geometries of linear and bent forms are shown below.<\/p>\n

\"003\"<\/a>\"001\"<\/a><\/p>\n

The relative free energy of the V-shaped bent form[7]<\/a><\/span> emerges as 3.5 kcal\/mol higher<\/strong> than the linear form[8]<\/a><\/span>. Now, to add a Grimme-D3 dispersion correction to the energies. The V-shape of the bent form now adopts the hairpin mode,[9]<\/a><\/span> and its energy is now 2.5 kcal\/mol lower<\/strong> than the linear form.[10]<\/a><\/span><\/p>\n

\"002\"<\/a><\/p>\n

Note in the above the very slight strange oscillation (kink) that appears about 11 atoms away from the hairpin bend. I repeated this with the wB97XD DFT procedure (in which dispersion is implicit) and found the same result.<\/p>\n

As triple-\u03b6 basis quality modelling of molecules with >100 atoms becomes increasingly common, it is worth repeating yet again that the model should always contain dispersion (and solvent if appropriate) corrections as default. Indeed, it is probably also worth re-investigating much early modelling (by this I mean modelling done ten or more years ago) to see if such corrections significantly influence the conclusions.[6]<\/a><\/span><\/p>\n

\n

\u2021<\/sup>The searches cannot be carried out according to the formula Cn<\/sub>H2n+2<\/sub>, but must be done individually for the value of n. I gave up at C50<\/sub>.<\/p>\n

References<\/h2>\n
  1. N.O.B. L\u00fcttschwager, T.N. Wassermann, R.A. Mata, and M.A. Suhm, \"The Last Globally Stable Extended Alkane\", Angewandte Chemie International Edition<\/i>, vol. 52, pp. 463-466, 2012. https:\/\/doi.org\/10.1002\/anie.201202894<\/a>\n\n<\/li>\n
  2. N. Cocherel, C. Poriel, J. Rault\u2010Berthelot, F. Barri\u00e8re, N. Audebrand, A. Slawin, and L. Vignau, \"New 3\u03c0\u20102Spiro Ladder\u2010Type Phenylene Materials: Synthesis, Physicochemical Properties and Applications in OLEDs\", Chemistry \u2013 A European Journal<\/i>, vol. 14, pp. 11328-11342, 2008. https:\/\/doi.org\/10.1002\/chem.200801428<\/a>\n\n<\/li>\n
  3. S.C. Nyburg, and A.R. Gerson, \"Crystallography of the even <i>n<\/i>-alkanes: structure of C<sub>20<\/sub>H<sub>42<\/sub>\", Acta Crystallographica Section B Structural Science<\/i>, vol. 48, pp. 103-106, 1992. https:\/\/doi.org\/10.1107\/s0108768191011059<\/a>\n\n<\/li>\n
  4. R. Boistelle, B. Simon, and G. P\u00e8pe, \"Polytypic structures of n-C28H58 (octacosane) and n-C36H74 (hexatriacontane)\", Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry<\/i>, vol. 32, pp. 1240-1243, 1976. https:\/\/doi.org\/10.1107\/s0567740876005025<\/a>\n\n<\/li>\n
  5. H.M.M. Shearer, and V. Vand, \"The crystal structure of the monoclinic form of n-hexatriacontant\", Acta Crystallographica<\/i>, vol. 9, pp. 379-384, 1956. https:\/\/doi.org\/10.1107\/s0365110x5600111x<\/a>\n\n<\/li>\n
  6. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-Garc\u00eda, M.J. Harvey, N.J. Mason, and H.S. Rzepa, \"The Houk\u2013List transition states for organocatalytic mechanisms revisited\", Chem. Sci.<\/i>, vol. 5, pp. 2057-2071, 2014. https:\/\/doi.org\/10.1039\/c3sc53416b<\/a>\n\n<\/li>\n
  7. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.978501<\/a>\n\n<\/li>\n
  8. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.978502<\/a>\n\n<\/li>\n
  9. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.978832<\/a>\n\n<\/li>\n
  10. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.978833<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    By about C17H36, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations. Indeed, a (co-crystal) of C16H34 shows it to have two-gauche bends..\u00a0Surprisingly, the longest linear alkane I was able to find a crystal structure for, C28H58\u00a0appears to be fully extended, (an early report of a low quality […]<\/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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[1171,24,1196,503],"ppma_author":[2661],"class_list":["post-12204","post","type-post","status-publish","format-standard","hentry","category-general","tag-dispersion","tag-energy","tag-relative-energy","tag-relative-free-energy"],"yoast_head":"\nModelling the geometry of unbranched alkanes. - 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=12204\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Modelling the geometry of unbranched alkanes. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"By about C17H36, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations. Indeed, a (co-crystal) of C16H34 shows it to have two-gauche bends..\u00a0Surprisingly, the longest linear alkane I was able to find a crystal structure for, C28H58\u00a0appears to be fully extended, (an early report of a low quality […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12204\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2014-03-29T15:35:03+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2014-03-31T16:12:50+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/003.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":"Modelling the geometry of unbranched alkanes. - 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=12204","og_locale":"en_GB","og_type":"article","og_title":"Modelling the geometry of unbranched alkanes. - Henry Rzepa's Blog","og_description":"By about C17H36, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations. 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But I have now noticed, largely through spotting Steve Bachrach's post on \"Acene dimers \u2013 open or closed?\" another geometric effect perhaps worthy of note, certainly one not always noted\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":24503,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24503","url_meta":{"origin":12204,"position":2},"title":"Molecule of the year 2021: Infinitene.","author":"Henry Rzepa","date":"December 16, 2021","format":false,"excerpt":"The annual \"molecule of the year\" results for 2021 are now available ... and the winner is Infinitene., This is a benzocirculene in the form of a figure eight loop (the infinity symbol), a shape which is also called a lemniscate after the mathematical (2D) function due to Bernoulli. The\u2026","rel":"","context":"In "Chiroptics"","block_context":{"text":"Chiroptics","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2644"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/12\/infinitene.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":8540,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8540","url_meta":{"origin":12204,"position":3},"title":"The mechanism of the Birch reduction. Part 3: reduction of benzene","author":"Henry Rzepa","date":"December 4, 2012","format":false,"excerpt":"Birch reduction of benzene itself results in 1,4-cyclohexadiene rather than the more stable (conjugated) 1,3-cyclohexadiene. Why is this? The mechanism, as elaborated in the previous two posts, involves a one-electron transfer from a sodium atom to form the radical anion, which is then protonated in a second step, and this\u2026","rel":"","context":"In \"Birch reduction\"","block_context":{"text":"Birch reduction","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=birch-reduction"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/12\/birch-ip.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","url_meta":{"origin":12204,"position":4},"title":"\u03c0-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?","author":"Henry Rzepa","date":"April 15, 2017","format":false,"excerpt":"Back in the early 1990s, we first discovered the delights of searching crystal structures\u00a0for unusual\u00a0bonding features. One of the first cases was a search for hydrogen bonds formed to the\u00a0\u03c0-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it's\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/04\/SQ-H-pi-1024x783.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":12224,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12224","url_meta":{"origin":12204,"position":5},"title":"What is the best way of folding a straight chain alkane?","author":"Henry Rzepa","date":"April 6, 2014","format":false,"excerpt":"In the previous post, I showed how modelling of unbranched alkenes depended on dispersion forces. When these are included, a bent (single-hairpin) form of C58H118 becomes lower in free energy than the fully extended linear form. Here I try to optimise these dispersion forces by adding further folds to see\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"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\/12204","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=12204"}],"version-history":[{"count":13,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12204\/revisions"}],"predecessor-version":[{"id":12221,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12204\/revisions\/12221"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=12204"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=12204"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=12204"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=12204"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}