{"id":2459,"date":"2020-10-23T16:06:19","date_gmt":"2020-10-23T07:06:19","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=2459"},"modified":"2021-02-10T10:11:00","modified_gmt":"2021-02-10T01:11:00","slug":"conformations-of-2-cyclohepten-1-one-tropilene","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2020\/10\/23\/conformations-of-2-cyclohepten-1-one-tropilene\/","title":{"rendered":"Conformations of 2-Cyclohepten-1-one (Tropilene)"},"content":{"rendered":"\n

\u30e1\u30e2.\u00a0<\/p>\n

Programs: Gromacs<\/a> (2020) on macOS Mojave (10.14.6); ORCA<\/a> (4.2.1) on CentOS Linux 7; WebMO<\/a> (20.0).<\/p>\n

Because tropilene is a pseudo-six-membered compound, it can exist as chair, twist-boat (skew-boat), boat, and half-chair forms. The microwave spectrum of the molecule was inconsistent with a chair form.1)<\/sup> Groenewald et al.<\/em> reported that a twist-half-boat or twist-half-chair (TH<\/strong>) form is the most stable form in the CCSD(T) level calculation and its rotational constants are close to the experimental values.2)<\/sup>\u00a0<\/p>\n

I generated conformers of tropilene by the simulated annealing method implemented in the Gromacs program with the GAFF2 force field and obtained four enantiomeric pairs: one chair (C<\/strong>) and three twist-boat (S<\/strong>) forms. In the PM7 level of theory, the 6<\/sup>S1<\/sub> (or 1<\/sup>S6<\/sub>) twist-boat form was converged to the chair form; on the other hand, in the density functional theory (DFT) level, the chair and 6<\/sup>S1<\/sub> (or 1<\/sup>S6<\/sub>) forms were converged to a half-chair (5<\/sup>H6<\/sub> and 6<\/sup>H5<\/sub>) form.\u00a0\u00a0Their relative energies at several DFT levels including B97-3c\/def2-mTZVP3)<\/sup> along with the reference CCSD(T) level2)<\/sup> were listed in the below table. Albeit not being successful to predict the global minimum, the low-cost B97-3c provided lower errors compared to the B3LYP\/6-31G(d) or the B3LYP\/6-311+G(d,p)2)<\/sup> level.<\/p>\n

\u00a0<\/p>\n

\"\"<\/p>\n\n\n\n\n\n\n\n

<\/strong>conformers<\/strong><\/td>\n		\u00a0Groenewald’s notation<\/strong>a<\/sup><\/em>
<\/strong><\/td>\n		\u0394G<\/em> (kcal mol\u22121<\/sup>)<\/strong>
<\/strong><\/td>\n<\/tr>\n
\n

B3LYP<\/strong><\/p>\n

\/6-31G(d)<\/strong><\/p>\n<\/td>\n

\n

B97-3c<\/strong><\/p>\n<\/td>\n

\n

\u03c9B97X-D3<\/strong><\/p>\n

\/6-31G(d)<\/strong><\/p>\n<\/td>\n

\n

\u03c9B97X-D3<\/strong><\/p>\n

\/6-311++G(d,p)<\/strong><\/p>\n

\u00a0<\/p>\n<\/td>\n

\n

M06-2X\/6-311+G(d,p)<\/strong><\/p>\n<\/td>\n

\n

RI-MP2\/cc-pVTZ<\/strong><\/p>\n<\/td>\n

CCSD(T)\/6-311+G(d,p)<\/strong>b<\/em><\/sup><\/td>\n<\/tr>\n
6<\/sup>H5<\/sub> and 5<\/sup>H6<\/sub><\/td>\nS6\/TH2<\/td>\n0.0<\/strong><\/td>\n0.0<\/strong><\/td>\n0.0<\/strong><\/td>\n0.0<\/strong><\/td>\n0.1<\/td>\n0.53<\/td>\n0.46<\/td>\n<\/tr>\n
1<\/sup>S4<\/sub> and 4<\/sup>S1<\/sub><\/td>\nTH6<\/td>\n0.8<\/td>\n0.4<\/td>\n0.1<\/td>\n0.1<\/td>\n0.0<\/strong><\/td>\n0.00<\/strong><\/td>\n0.00<\/strong><\/td>\n<\/tr>\n
7<\/sup>S2,3<\/sub> and 2,3<\/sup>S7<\/sub><\/td>\nH2\/TH5<\/td>\n1.2<\/td>\n0.9<\/td>\n0.6<\/td>\n0.6<\/td>\n0.6<\/td>\n0.52<\/td>\n0.56<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

a<\/em><\/sup> H, half-chair or half-boat (five atoms are approximately in a plane); S, sofa (six atoms are approximately in a plane); T, twist- .2)<\/sup> b<\/em><\/sup>\u00a0<\/sup><\/em>Cited from Ref. 2.<\/p>\n

Note:<\/p>\n

ORCA input options for the meta-hybrid GGA M06-2X functional.<\/p>\n

! M062X 6-311+G(d,p) \n! OPT\n! NumFreq\n\n! Grid6 NoFinalGrid\n%method IntAcc 12 end\n%geom Calc_Hess true; NumHess true end<\/pre>\n
\u00a0<\/p>\n
References<\/strong><\/p>\n
    \n
  1. Kitchin, R. W., et al<\/em>., The microwave spectrum, dipole moment, and molecular conformation of 2-cycloheptene-1-one. J. Mol. Spectrosc<\/em>. 1979<\/strong>, 75<\/em>, 429-439. doi: 10.1016\/0022-2852(79)90086-9<\/a>.<\/li>\n
  2. Groenewald F., et al<\/em>., A computational investigation of the effect of the double bond on the conformations of seven membered rings. Struct. Chem<\/em>. 2013<\/strong>, 24<\/em>, 243\u2013250. doi: 10.1007\/s11224-012-0073-4<\/a>.<\/li>\n
  3. Brandenburg, J. G., et al<\/em>., B97-3c: A revised low-cost variant of the B97-D density functional method. J. Chem. Phys<\/em>. 2018<\/strong>, 148<\/em>, 064104. doi: 10.1063\/1.5012601<\/a>.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":2502,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"","_original_post":"","footnotes":""},"categories":[5],"tags":[],"class_list":["post-2459","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-5","ja"],"aioseo_notices":[],"aioseo_head":"\n\t\t\n\t\n\t\n\t\n\t\n\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t\n\t\t