{"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:\/\/rzepa.net\/blog\/2014\/04\/06\/what-is-the-best-way-of-folding-a-straight-chain-alkane\/","title":{"rendered":"What is the best way of folding a straight chain alkane?"},"content":{"rendered":"

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[cite]10.1021\/jp064811m[\/cite], 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.[cite]10.6084\/m9.figshare.988335[\/cite]<\/p>\n

\"Click
Click for 3D<\/figcaption><\/figure>\n

One folded at a slightly different point (below) was in fact higher 4.7 kcal\/mol in energy that the single hairpin,[cite]10.6084\/m9.figshare.988334[\/cite] indicating that there is an optimum position for the bend.<\/p>\n

\"Click
Click for 3D<\/figcaption><\/figure>\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[cite]10.6084\/m9.figshare.988771[\/cite] is 1.6<\/del>\u00a02.5 kcal\/mol lower<\/strong> than the single-hairpin. It did not feature in the previous report[cite]10.1021\/jp064811m[\/cite] 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<\/figcaption><\/figure>\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[cite]10.6084\/m9.figshare.988333[\/cite] (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<\/figcaption><\/figure>\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","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":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[902,922,930,1038,1512],"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"],"_links":{"self":[{"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/posts\/12224","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/comments?post=12224"}],"version-history":[{"count":0,"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/posts\/12224\/revisions"}],"wp:attachment":[{"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/media?parent=12224"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/categories?post=12224"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/rzepa.net\/blog\/wp-json\/wp\/v2\/tags?post=12224"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}