Determination of absolute configuration using X-ray diffraction

Methods for determination of absolute structure using X-ray crystallography are described, with an emphasis on applications for absolute configuration assignment of enantiopure light-atom organic compounds. The ability to distinguish between alternative absolute structures by X-ray crystallography is the result of a physical phenomenon called resonant scattering, which introduces small deviations from the inherent inversion symmetry of single-crystal X-ray diffraction patterns. The magnitude of the effect depends on the elements present in the crystal and the wavelength of the X-rays used to collect the diffraction data, but it is always very weak for crystals of compounds containing no element heavier than oxygen. The precision of absolute structure determination by conventional least squares refinement appears to be unduly pessimistic for light-atom materials. Recent developments based on Bijvoet differences, quotients and Bayesian statistics enable better and more realistic precision to be obtained. The new methods are sensitive to statistical outliers, and techniques for identifying these are summarised.     

Determination of the absolute configuration of peptide natural products by using stable isotope labeling and mass spectrometry

Structure elucidation of natural products including the absolute configuration is a complex task that involves different analytical methods like mass spectrometry, NMR spectroscopy, and chemical derivation, which are usually performed after the isolation of the compound of interest. Here, a combination of stable isotope labeling of Photorhabdus and Xenorhabdus strains and their transaminase mutants followed by detailed MS analysis enabled the structure elucidation of novel cyclopeptides named GameXPeptides including their absolute configuration in crude extracts without their actual isolation.     

Determination of the absolute configuration of the diterpene tonantzitlolone B

In this work synthetic and semi-synthetic studies toward the antitumor active natural product tonantzitlolone B are described, starting with an advanced intermediate obtained from the total synthesis of tonantzitlolone and a natural sample of this compound, respectively. The unknown absolute configuration of the stereogenic center in the side chain was elucidated to be (R).     

Synthetic studies toward verrucosidin: Determination of the absolute configuration

The tetrahydrofuran portion 3 of verrucosidin 1, a potent neurotoxin, is synthesized in an enantiomerically pure form via the stereoselective osmylation of the chiral hydroxy diene ester 5 as a key step.     

Synthesis of an advanced intermediate en route to the mitomycin natural products

[Structure: see text] An advanced intermediate in our planned synthesis of mitomycin C has been acquired in nine steps from tert-butyl glyoxylate. The aziridinyl pyrrolidine and quinone subunits are coupled regioselectively to arrive at an enamine that is prepared for C10 homologation.     

Synthesis and absolute configuration of brevione B, an allelochemical isolated from Penicillium sp.

Breviones A-E (1-5), allelochemicals isolated from Penicillium brevicompactum Dierckx, are structurally unique diterpenoid derivatives. The first synthesis of both enantiomers of brevione B (2) was accomplished by employing the double S_N2′-type tandem reaction as a key step, and the absolute configuration of the naturally occurring 2 was established.     

Determination of the absolute configuration of three as-hydrindacene compounds by vibrational circular dichroism

[Structure: see text]. The absolute configurations of three compounds with a rigid 1,8-disubstituted as-hydrindacene skeleton have been determined using vibrational circular dichroism spectroscopy and quantum chemical calculations. Experimental spectra were compared to B3LYP/6-31G and B3LYP/cc-pVTZ level predicted spectra. Based on the agreement between the predicted and experimental spectra, the stereochemistry could be assigned with high confidence. The results were found to be in agreement with ECD determinations and/or predictions based on the applied asymmetric methods in the synthetic route.     

Determination of the absolute configuration of carbohydrate components of flavonol glycosides of the chestnut

Conclusions On the basis of the rates of their acid hydrolysis, their optical activities, and their IR spectra, it has been established that the glycosides ofAesculus hippocastanum L. are (SK-1) 3--L-arabofuranosyloxy-5,7,4-trihydroxyflavone, (SK-2) 3--L-rhamnofuranosyloxy-5,7,4-trihydroxyflavone, (SK-3) 3--L-arabofuranosyloxy-5,7,3,4-tetrahydroxyflavone, and (SK-4) 3--L-rhamnofuranosyloxy-5,7,3,4-tetrahydroxyflavone.The glycoside SK-3 is identical with avicularin isolated from the leaves ofPsidium quajava [5]. The complete structures of the other three glycosides have been established for the first time.Khimiya Prirodnykh Soedinenii, Vol. 5, No. 1, pp. 5–7, 1969     

皂素皂苷脂肪链中甲基绝对构型的确定

利用Sharpless环氧化和Roush反应合成了皂素苷脂肪链中C9脂肪酸单体的两个非对映异构体,即(3S,5S,6S)-3,5-二羟基-6-甲基-δ-辛酸内酯和(3S,5S,6R)-3,5-二羟基-6-甲基-δ-辛酸内酯。通过与天然样品进行理化数据对比,确定了皂素皂苷脂肪链中甲基的绝对构型为S。     

Perturbation theory to determine the stable isomer of triatomic linear molecules

The electronegativity perturbation theory up to the fourth order has been used to study the preferred isomer of linear triatomic molecules. Systems with 10–16 valence–electron systems are discussed and our results are in good agreement with the experiment. The only exception is the isomers of PNO. The usefulness of the perturbation theory is briefly discussed. © 1993 John Wiley & Sons, Inc.     

Ab initio study of the Trinem antibiotic Sanfetrinem GV104326

We present a theoretical calculation of trinem antibiotic sanfetrinem GV104326 and its cis-isomer of proton in β-lactam ring and methoxy inversion isomer. Ab initio Hartree Fock method is employed to calculate the geometry optimization; optimized parameters, bond lengths, bond angles and dihedral angles of isomers. We also calculated the vibrational frequencies, the IR intensities, the Raman activities and the thermochemical parameters. Mulliken population analysis is used to compare bond strength of an active site. These results are compared with available experimental data and other related theoretical calculations. The calculated IR spectra are in good agreement with experiments. Calculated geometrical and conformational structures of sanfetrinem and its isomers support the previous study of the geometrical requirements for the antibacterial activities. The significance of the rotational conformation of the carboxyl group to chemical reactivities is discussed.     

Circular dichroism of tail-to-tail bisbenzyliso-quinoline and the absolute configuration of daurisoline isolated from Menispermum dauricum

Since two asymmetric centres are usually present in the bisbenzylisoquinolines, the circular dichroism is known to be an important method to elucidate their stereochemistry. We studied the relationships of the CD spectra with the stereochemistry of synthetic RR-(1), SS-(2), RS-daurisoline (3) and SR-daurisoline (4). By comparision of the CD spectrum of natural daurisoline (1) from Menispermum dauricum (Menispermaceae) with those of synthetic enantiomers, the absolute configuration was established as RR-daurisoline (1).     

Determination of the absolute configuration of the asymmetric center at C11 in the eudesmanolides

It has been shown that it is possible to use the method of circular dichroism to determine the absolute configuration of the asymmetric center at C₁₁ in the eudesmanolides. The orientations of the hydroxy group at C₁ and of the methyl group at C₄ in arabsin have been established.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 343–346, May–June, 1980.     

Determination of the steric configuration of organic compounds with the aid of stable iminoxyls

Conclusions A new method was proposed for determining the steric configuration of organic compounds, using a free radical label.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1137–1139, May, 1967.     

Determination of the absolute configuration of sialic acids in gangliosides from the sea cucumber Cucumaria echinata

Enantiomeric pairs of sialic acid, D- and L-NeuAc (N-acetylneuraminic acid), were converted to D- and L-arabinose, respectively, by chemical degradation. Using this method, the absolute configuration of the sialic acid residues, NeuAc and NeuGc (N-glycolylneuraminic acid), in the gangliosides from the sea cucumber Cucumaria echinata was determined to be the D-form. Although naturally occurring sialic acids have been believed to be the D-form on the basis of biosynthetic evidence, this is the first report of the determination of the absolute configuration of the sialic acid residues in gangliosides using chemical methods.