The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.
Stereochemical studies of a cruciferous oxindole phytoalexin, (S)-(-)-spirobrassinin [(-)-4], and its oxazoline analogue, spirooxazoline (11), were carried out. Racemic spirobrassinin [(+/-)-4] was synthesized by SOCl(2)- or MsCl-mediated cyclization of dioxibrassinin [(+/-)-8]. Treatment of (3-hydroxyoxindol-3-yl)methylammonium chloride [(+/-)-9] with CSCl(2) and subsequent methylation of the obtained spirooxazolidinethione (+/-)-10 afforded spirooxazoline [(+/-)-11]. Enantioresolution of (+/-)-4 and (+/-)-11 was achieved by derivatization with (S)-(-)-1-phenylethyl isocyanate (12), chromatographic separation of diastereomeric amides 13, 14 or 15, 16, and their cleavage with CH(3)ONa. Absolute configuration of the stereogenic center in natural (S)-(-)-4 was derived from the exciton, calculated via CD methods, and unequivocally confirmed by X-ray crystallographic analyses of 1-[1'S,4'R-(-)-camphanoyl] derivatives [(-)-19 and (-)-20] of (+)- and (-)-4. Novel enantiomeric enrichment phenomena of 4 and 11 were discovered during their chromatographic separations under achiral HPLC conditions. Screening of antifungal activity against the fungus Bipolaris leersiae revealed no significant dependence of this activity on absolute configuration.
A naturally occurring 1,1'-biphenanthrene, blestriarene C (1), was prepared in 13 steps and 30% overall yield. The key steps are the ester-mediated nucleophilic aromatic substitution on 2,6-di-tert-butyl-4-methoxyphenyl 5-isopropoxy-2-methoxybenzoate (4) by 2-methoxy-4-methoxymethoxy-6-methylphenylmagnesium bromide (5) and a novel intramolecular cyclization of the resulting 4-isopropoxy-2'-methoxy-4'-methoxymethoxy-6'-methylbiphenyl-2-carboxylic ester 14 to 7-isopropoxy-4-methoxy-2-(methoxymethoxy)phenanthren-9-ol (15). The racemic blestriarene C was optically resolved by chiral HPLC on a preparative scale to give several 10-mg yields of both the enantiomers in up to 95% ee. The absolute stereochemistry was determined to be S(a)-(-) by the axial chirality recognition method, which was based on the stereospecific formation of a 12-membered cyclic diester containing two biaryl-o,o'-diyl unites joined by ester -CO(2)- linkages. The validity of the method was confirmed by an X-ray crystallographic analysis and ab initio conformational analyses of such 12-membered cyclic diesters. It was found that blestriarene C and its 7,7'-diisopropyl ether 2 underwent rapid photoracemization even under ambient light exposure.
Geometrical structures of the isolated benzene and naphthalene molecules have been accurately determined by using ultrahigh-resolution laser spectroscopy and ab initio calculation in a complementary manner. The benzene molecule has been identified to be planar and hexagonal (D(6h)) and the structure has been determined with accuracies of 2 × 10(-14) m (0.2 mÅ; 1 Å = 1 × 10(-10) m) for the C-C bond length and 1.0 × 10(-13) m (1.0 mÅ) for the C-H bond length. The naphthalene molecule has been identified to be symmetric with respect to three coordinate axes (D(2h)) and the structure has been determined with comparable accuracies. We discuss the effect of vibrational averaging that is a consequence of zero-point motions on the uncertainty in determining the bond lengths.
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