{"id":12224,"date":"2014-04-06T08:56:44","date_gmt":"2014-04-06T07:56:44","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=12224"},"modified":"2014-04-06T08:56:44","modified_gmt":"2014-04-06T07:56:44","slug":"what-is-the-best-way-of-folding-a-straight-chain-alkane","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/blog\/?p=12224","title":{"rendered":"What is the best way of folding a straight chain alkane?"},"content":{"rendered":"
\n

In the previous post<\/a>, I showed how modelling of unbranched alkenes depended on dispersion forces. When these are included, a bent (single-hairpin) form of C58<\/sub>H118<\/sub> 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 what happens.<\/p>\n

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

I had noted a small kink in the bent single-hairpin form (above, red circle). What about making a full bend at that point? Such forms have been previously investigated using OPLS-AA mechanics[1]<\/a><\/span>, with the finding that such a triple-hairpin conformation (below) was 9.7 kcal\/mol higher<\/strong> in energy than the single hairpin (above). OK, its got eight gauche-turns more (four per bend, and which do cost energy), but it also has three rather than just one row of close dispersion-stabilising contacts to compensate. Using quantum rather than molecular mechanics (B3LYP+D3\/TZVP), I found that this triple-hairpin folded form was 3.2 kcal\/mol higher in free energy than the single hairpin.[2]<\/a><\/span><\/p>\n

\"Click

Click for 3D<\/p><\/div>\n

One folded at a slightly different point (below) was in fact higher 4.7 kcal\/mol in energy that the single hairpin,[3]<\/a><\/span> indicating that there is an optimum position for the bend.<\/p>\n

\"Click

Click for 3D<\/p><\/div>\n

I was convinced better folds could be found. So how about this double-hairpin, but in three dimensions to form a prism<\/strong> so that each chain has just as many contacts as the triple-hairpin, but is achieved with two-fewer gauche-turns? Its free energy[4]<\/a><\/span> is 1.6<\/del>\u00a02.5 kcal\/mol lower<\/strong> than the single-hairpin. It did not feature in the previous report[1]<\/a><\/span> and hence represents a new lowest-energy folding (the colour indicates three ribbons of attractive non-covalent interactions, using the\u00a0NCI technique). I would point out that such “manual” searching for better folds is not really sustainable; a statistical method would normally be used (MD or Monte-Carlo).<\/p>\n

\"Click

Click for 3D<\/p><\/div>\n

A similarly folded version of the triple-hairpin can be made (below), with more opportunity for five rows of close dispersion contacts. This time however, the free energy is 1.9 kcal\/mol higher than the single hairpin[5]<\/a><\/span> (but the position of the fold does need to be optimised and perhaps a better one can be found).\u00a0This result does imply that there is an optimum balance between the energy penalty of creating four gauche-turns per fold and the additional energy stabilisation of the dispersion. Perhaps the triple hair-pin above is close to that optimum?<\/p>\n

\"Click

Click for 3D<\/p><\/div>\n

Unfortunately no crystal structures for the higher linear alkanes have been reported that would give us a reality check on any of these models. Can it really be that difficult to crystallise such molecules?<\/p>\n

References<\/h2>\n
  1. L.L. Thomas, T.J. Christakis, and W.L. Jorgensen, \"Conformation of Alkanes in the Gas Phase and Pure Liquids\", The Journal of Physical Chemistry B<\/i>, vol. 110, pp. 21198-21204, 2006. https:\/\/doi.org\/10.1021\/jp064811m<\/a>\n\n<\/li>\n
  2. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.988335<\/a>\n\n<\/li>\n
  3. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.988334<\/a>\n\n<\/li>\n
  4. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.988771<\/a>\n\n<\/li>\n
  5. H.S. Rzepa, \"Gaussian Job Archive for C58H118\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.988333<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    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 what happens. I had noted […]<\/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,"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":[4],"tags":[147,1186,1187,164,1185],"class_list":["post-12224","post","type-post","status-publish","format-standard","hentry","category-general","tag-energy","tag-energy-penalty","tag-energy-stabilisation","tag-free-energy","tag-lowest-energy-folding"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p1gPyz-3ba","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12224","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=12224"}],"version-history":[{"count":0,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12224\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=12224"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=12224"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=12224"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}