Absolute Configuration Analysis Research Articles

Catalytic Asymmetric Synthesis of Silicon‐Stereogenic Dihydrodibenzosilines: Silicon Central‐to‐Axial Chirality Relay

AbstractA Rh‐catalyzed asymmetric synthesis of silicon‐stereogenic dihydrodibenzosilines featuring axially chiral 6‐membered bridged biaryls is demonstrated. In the presence of a RhI catalyst with a chiral diphosphine ligand, a wide range of dihydrodibenzosilines containing both silicon‐central and axial chiralities are conveniently constructed in excellent enantioselectivities via dehydrogenative C(sp3)−H silylation. Absolute configuration analysis by single‐crystal X‐ray structures revealed a novel silicon central‐to‐axial chirality relay phenomenon, which we believe will inspire further research in the field of asymmetric catalysis and chiroptical materials.

Catalytic Asymmetric Synthesis of Silicon-Stereogenic Dihydrodibenzosilines: Silicon Central-to-Axial Chirality Relay.

A Rh-catalyzed asymmetric synthesis of silicon-stereogenic dihydrodibenzosilines featuring axially chiral 6-membered bridged biaryls is demonstrated. In the presence of a RhI catalyst with a chiral diphosphine ligand, a wide range of dihydrodibenzosilines containing both silicon-central and axial chiralities are conveniently constructed in excellent enantioselectivities via dehydrogenative C(sp3 )-H silylation. Absolute configuration analysis by single-crystal X-ray structures revealed a novel silicon central-to-axial chirality relay phenomenon, which we believe will inspire further research in the field of asymmetric catalysis and chiroptical materials.

Structural analysis of the O-antigen polysaccharide from Escherichia coli O188

The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis revealed d-Man, d-Glc, d-GlcN and d-GlcA as major components. The structure of the O-specific polysaccharide was determined using one- and two-dimensional 1H and 13C NMR spectroscopy experiments, where inter-residue correlations were identified by 1H,13C-heteronuclear multiple-bond correlation and 1H,1H-NOESY experiments, which revealed that it consists of pentasaccharide repeating units with the following structure: ▪Biosynthetic aspects and NMR analysis are consistent with the presented structure as the biological repeating unit. The O-antigen of Shigella boydii type 16 differs only in that it carries O-acetyl groups to ~50% at O6 of the branch-point mannose residues. A molecular model of the E. coli O188 O-antigen containing 20 repeating units extends ~100 Å, which is similar to the height of the periplasmic portion of polysaccharide co-polymerase Wzz proteins that regulate the O-antigen chain length of lipopolysaccharides in the Wzx/Wzy biosynthetic pathway.

Isolation and characterization of a novel exopolysaccharide secreted by Lactobacillus mucosae VG1

A novel strain of Lactobacillus mucosae was isolated from a faecal sample of an individual who had adhered to a strict vegetarian diet for nine years. The strain displayed a ropy character when grown on plates and generated a relatively small amount (62 mg/L) of an exopolysaccharide (EPS) when grown in broth culture.The EPS eluted from a size exclusion chromatography column as a single band with a weight average molecular mass of 1.51 × 104 g/mol. Monomer analysis and sugar absolute configuration analysis confirmed that the EPS was a D-galactan. Using linkage analysis in combination with 1D and 2D-NMR spectroscopy, with spectra being recorded for both the native EPS and for the products generated by Smith degradation of the EPS, the following structure was determined for the repeat unit of the polysaccharide: [Display omitted] This is a novel D-galactan and represents the first structure for an EPS produced by a strain of Lactobacillus mucosae to be reported.

Trichophycins B-F, Chlorovinylidene-Containing Polyketides Isolated from a Cyanobacterial Bloom.

NMR-guided isolation (based on 1D 1H and 13C NMR resonances consistent with a chlorovinylidene moiety) resulted in the characterization of five new highly functionalized polyketides, trichophycins B-F (1-5), and one nonchlorinated metabolite tricholactone (6) from a collection of Trichodesmium bloom material from the Gulf of Mexico. The planar structures of 1-6 were determined using 1D and 2D NMR spectroscopy, mass spectrometry, and complementary spectroscopic procedures. Absolute configuration analysis of 1 and 2 were carried out by 1H NMR analysis of diastereomeric Mosher esters in addition to ECD spectroscopy, J-based configuration analysis, and DFT calculations. The absolute configurations of 3-6 were proposed on the basis of comparative analysis of 13C NMR chemical shifts, relative configurations, and optical rotation values to compounds 1 and 2. Compounds 1-5 represent new additions to the trichophycin family and are hallmarked by a chlorovinylidene moiety. These new trichophycins and tricholactone (1-6) feature intriguing variations with respect to putative biosynthetic starting units, halogenation, and terminations, and trichophycin E (4) features a rare alkynyl bromide functionality. The phenyl-containing trichophycins showed low cytotoxicity to neuro-2A cells, while the alkyne-containing trichophycins showed no toxicity.

Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-16000

The structure of a polysaccharide from Vibrio parahaemolyticus strain AN-16000 has been investigated. The sugar and absolute configuration analysis revealed d-Glc, d-GalN, d-QuiN and l-FucN as major components. The PS was subjected to dephosphorylation with aqueous 40% HF to obtain an oligosaccharide that was analyzed by 1H and 13C NMR spectroscopy. The HR-MS spectrum of the oligosaccharide revealed a pentasaccharide composed of two Glc residues, one QuiNAc and one GalNAc, one FucNAc, as well as a glycerol moiety. The structure of the PS was determined using 1H, 13C, 15N and 31P NMR spectroscopy; inter-residue correlations were identified by 1H,13C-heteronuclear multiple-bond correlation, 1H,1H-NOESY and 1H,31P-hetero-TOCSY experiments. The PS backbone has the following teichoic acid-like structure: →3)-d-Gro-(1-P-6)-β-d-Glcp-(1→4)-α-l-FucpNAc-(1→3)-β-d-QuipNAc-(1→ with a side-chain consisting of α-d-Glcp-(1→6)-α-d-GalpNAc-(1→ linked to the O3 position of the FucNAc residue.

DETERMINATION OF THE ABSOLUTE CONFIGURATION OF NEW PIPERIDIN-4-ONE DERIVATIVE FROM Pellacalyx saccardianus BY NOESY SPECTROSCOPY

A new alkaloid, pellacalyxin was isolated from the leaves of Pellacalyx saccardianus of Rhizophoraceae family. Pellacalyxin was analyzed using nuclear Overhauser spectroscopy (NOESY) nuclear magnetic resonance (NMR) technique to determine the absolute configuration. The analysis of absolute configuration of pellacalyxin was supported by X-ray crystallography. 1H-1H NOESY NMR spectroscopy exhibited that pellacalyxin possesses two chiral centers (3S) and (6R).

Elucidation of the absolute configuration of rhizopine by chiral supercritical fluid chromatography and vibrational circular dichroism.

The absolute configuration of rhizopine, an opine-like natural product present in nitrogen-fixing nodules of alfalfa infected by rhizobia, is elucidated using a combination of state-of-the-art analytical and semi-preparative supercritical fluid chromatography and vibrational circular dichroism spectroscopy. A synthetic peracetylated racemate was fractionated into its enantiomers and subjected to absolute configuration analysis revealing that natural rhizopine exists as a single enantiomer. The stereochemistry of non-derivatized natural rhizopine corresponds to (1R,2S,3R,4R,5S,6R)-4-amino-6-methoxycyclohexane-1,2,3,5-tetraol.

Structure determination of the neutral exopolysaccharide produced by Lactobacillus delbrueckii subsp. bulgaricus OLL1073R-1

The neutral exopolysaccharide (NPS) of Lactobacillus delbrueckii subsp. bulgaricus strain OLL1073R-1 was purified and characterized. The molecular mass was 5.0×106 g/mol. Sugar and absolute configuration analyses gave the following composition: d-Glc, 1; d-Gal, 1.5. The NPS was also submitted to periodate oxidation followed by borohydride reduction and Smith degradation. Sugar and methylation analyses, 1H and 13C nuclear magnetic resonance, and mass spectrometry of the NPS or of its specifically modified products allowed determining the repeating unit sequence: {2)Glc(α1–3)Glc(β1–3)[Gal(β1–4)]Gal(β1–4)Gal(α1–}n. The structure is compared to that of exopolysaccharides produced by other Lactobacillus bulgaricus strains.

単結晶X線回折と有機化合物の絶対配置決定

単結晶X線回折と有機化合物の絶対配置決定

Reconciliation of Chemical, Enzymatic, Spectroscopic and Computational Data To Assign the Absolute Configuration of the DNA Base Lesion Spiroiminodihydantoin

The diastereomeric spiroiminodihydantoin-2'-deoxyribonucleoside (dSp) lesions resulting from 2'-deoxyguanosine (dG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG) oxidation have generated much attention due to their highly mutagenic nature. Their propeller-like shape leads these molecules to display mutational profiles in vivo that are stereochemically dependent. However, there exist conflicting absolute configuration assignments arising from electronic circular dichroism (ECD) and NOESY-NMR experiments; thus, providing definitive assignments of the 3D structure of these molecules is of great interest. In the present body of work, we present data inconsistent with the reported ECD assignments for the dSp diastereomers in the nucleoside context, in which the first eluting isomer from a Hypercarb HPLC column was assigned to be the S configuration, and the second was assigned the R configuration. The following experiments were conducted: (1) determination of the diastereomer ratio of dSp products upon one-electron oxidation of dG in chiral hybrid or propeller G-quadruplexes that expose the re or si face to solvent, respectively; (2) absolute configuration analysis using vibrational circular dichroism (VCD) spectroscopy; (3) reinterpretation of the ECD experimental spectra using time-dependent density functional theory (TDDFT) with the inclusion of 12 explicit H-bonding waters around the Sp free bases; and (4) reevaluation of calculated specific rotations for the Sp enantiomers using the hydration model in the TDDFT calculations. These new insights provide a fresh look at the absolute configuration assignments of the dSp diastereomers in which the first eluting from a Hypercarb-HPLC column is (-)-(R)-dSp and the second is (+)-(S)-dSp. These assignments now provide the basis for understanding the biological significance of the stereochemical dependence of enzymes that process this form of DNA damage.

Structure determination ofStreptococcus suisserotype 14 capsular polysaccharide

The capsular polysaccharide (CPS) of Streptococcus suis serotype 14 was purified, chemically modified, and characterized. Sugar and absolute configuration analyses gave the following CPS composition: d-Gal, 3; d-Glc, 1; d-GlcNAc, 1; d-Neu5Ac, 1. The Sambucus nigra lectin, which recognizes the Neu5Ac(α2–6)Gal/GalNAc sequence, showed binding to the native CPS. Sialic acid was found to be terminal, and the CPS was quantitatively desialylated by mild acid hydrolysis. It was also submitted to periodate oxidation followed by borohydride reduction and Smith degradation. Sugar and methylation analyses,1H and13C nuclear magnetic resonance, and mass spectrometry of the native CPS or of its specifically modified products allowed to determine the repeating unit sequence: [6)[Neu5Ac(α2–6)Gal(β1–4)GlcNAc(β1–3)]Gal(β1–3)Gal(β1–4)Glc(β1–]n. S. suis serotype 14 CPS has an identical sialic acid-containing side chain as serotype 2 CPS, but differs by the absence of rhamnose in its composition. The same side chain is also present in group B Streptococcus type Ia CPS, except that in the latter sialic acid is 2,3- rather than 2,6-linked to the following galactose. A correlation between the S. suis CPS sequence and genes of the serotype 14 cps locus encoding putative glycosyltransferases and polymerase responsible for the biosynthesis of the repeating unit is proposed.

Structure Elucidation and Absolute Stereochemistry of Isomeric Monoterpene Chromane Esters

Six novel monoterpene chromane esters were isolated from the aerial parts of Peperomia obtusifolia (Piperaceae) using chiral chromatography. This is the first time that chiral chromane esters of this kind, ones with a tethered chiral terpene, have been isolated in nature. Due to their structural features, it is not currently possible to assess directly their absolute stereochemistry using any of the standard classical approaches, such as X-ray crystallography, NMR, optical rotation, or electronic circular dichroism (ECD). Herein we report the absolute configuration of these molecules, involving four chiral centers, using vibrational circular dichroism (VCD) and density functional theory (DFT) (B3LYP/6-31G*) calculations. This work further reinforces the capability of VCD to determine unambiguously the absolute configuration of structurally complex molecules in solution, without crystallization or derivatization, and demonstrates the sensitivity of VCD to specify the absolute configuration for just one among a number of chiral centers. We also demonstrate the sufficiency of using the so-called inexpensive basis set 6-31G* compared to the triple-ζ basis set TZVP for absolute configuration analysis of larger molecules using VCD. Overall, this work extends our knowledge of secondary metabolites in plants and provides a straightforward way to determine the absolute configuration of complex natural products involving a chiral parent moiety combined with a chiral terpene adduct.

Reliability of computed signs and intensities for vibrational circular dichroism spectra

We present in detail a novel measure that improves the reliability of the assignment procedure for vibrational circular dichroism (VCD) spectra extending the useful robustness concept introduced by Nicu and Baerends. This measure enables spectroscopists to single out bands with unreliable VCD intensities that can be disregarded during analysis and determination of absolute configuration. The previously proposed robustness criterion is shown to be gauge dependent and less reliable than the one proposed here.

Absolute configuration determination of isoflavan-4-ol stereoisomers

Elucidation of the correct stereochemistry of the metabolite is essential for the mechanistic study of bioactive compounds. Isoflavan-4-ol has the same chiropical chromophore as THD, the biosynthetic precursor of the potent phytoestrogen S-equol. Interested in the correct absolute configuration of isoflavan-4-ol stereoisomers and to compare the available practical approaches for the absolute configuration determination, complete absolute configuration analysis of isoflavan-4-ol stereoisomers has been carried out with by means of ECD and VCD spectroscopy as well as modified Mosher method. Theoretical TD-DFT computations resulted in a poor simulation of the observed experimental ECD spectra, and thus inconclusive absolute configuration assignments of isoflavan-4-ol stereoisomers were obtained. However, DFT-assisted VCD spectroscopic analyses successfully determined correct absolute configurations, and further confirmed by modified Mosher method.

ChemInform Abstract: Absolute Structure and Absolute Configuration

Fundamental notions concerning absolute structure and absolute configuration, and their determination from single-crystal diffraction measurements, are presented and reviewed. A glossary of terms with definitions useful in this field is provided. For absolute structure and its determination, the separate but interacting influences of the structure and the inversion-distinguishing power of an X-ray diffraction experiment with dispersive scatterers are examined. Important experimental and algorithmic details of the current methods used for absolute-structure determination are provided. Characterization of crystals for absolute-structure determination and of molecules for absolute-configuration determination are treated. Attention is given to the analysis of absolute structure and absolute configuration in twinned crystals.

Structure determination ofStreptococcus suisserotype 2 capsular polysaccharide

The capsular polysaccharide (CPS) of Streptococcus suis serotype 2 was isolated, purified, chemically modified, and characterized. Sugar and absolute configuration analyses of the CPS gave the following composition: D-Gal, 3; D-Glc, 1; D-GlcNAc, 1; D-Neu5Ac, 1; L-Rha, 1. Sialic acid was found to be terminal, and the CPS was quantitatively desialylated by mild acid hydrolysis. The CPS was also submitted to periodate oxidation followed by borohydride reduction and Smith degradation. Sugar and methylation analysis, 1H and 13C nuclear magnetic resonance, and mass spectrometry of the native CPS or of its specifically modified products allowed to determine the repeating unit sequence: [4)[Neu5Ac(alpha2-6)Gal(beta1-4)GlcNAc(beta1-3)]Gal(beta1-4)[Gal(alpha1-3)]Rha(beta1-4)Glc(beta1-]n. The backbone sequence was found to be identical to that of Streptococcus agalactiae or group B Streptococcus (GBS) type VIII and Streptococcus pneumoniae type 23F. The S. suis CPS shares the sequence Neu5Ac-Gal-GlcNAc-Gal in common with GBS types Ia, Ib, II, III, and IV CPSs but differs from them by the presence of rhamnose and the fact that sialic acid is 2,6- rather than 2,3-linked to the following Gal. A correlation between the S. suis CPS sequence and genes of the serotype 2 cps locus encoding putative enzymes responsible for the biosynthesis of the repeating unit was tentatively established.

Convergence of the 5-LOX and COX-2 pathways: heme-catalyzed cleavage of the 5S-HETE-derived di-endoperoxide into aldehyde fragments

Oxygenation of the 5-lipoxygenase product 5S-hydroxyeicosatetraenoic acid by cyclooxygenase-2 yields a bicyclic di-endoperoxide. The di-endoperoxide contains two peroxides spanning from carbons 9 to 11 and 8 to 12, and two hydroxyls at carbons 5 and 15 of arachidonic acid (Schneider C., et al. 2006. Convergent oxygenation of arachidonic acid by 5-lipoxygenase and cyclooxygenase-2. J. Am. Chem. Soc. 128: 720). Here, we report that treatment of the di-endoperoxide with hematin or ferrous chloride results in cleavage of both peroxide O-O bonds and of the bonds between the carbons that carry the peroxide groups, producing the aldehydes 4-hydroxy-2E-nonenal (4-HNE), 8-oxo-5S-hydroxy-6E-octenoic acid, and malondialdehyde (MDA). The hematin- and ferrous iron-catalyzed transformation of the di-endoperoxide proceeded with a similar yield of products as the cleavage of the prostaglandin endoperoxide PGH(2) to 12S-hydroxy-5Z,8E,10E-heptadecatrienoic acid and MDA. Chiral phase HPLC analysis of the 4-HNE cleavage product showed greater than 98% 4S and thus established the S configuration of the 15-carbon of the di-endoperoxide that had not previously been assigned. This transformation of the 5-lipoxygenase/cyclooxygenase-2 derived di-endoperoxide invokes the possibility of a novel pathway to formation of the classic lipid peroxidation products 4-HNE and MDA.

ChemInform Abstract: Four Pimarane Diterpenes from Marine Fungus: Chloroform Incorporated in Crystal Lattice for Absolute Configuration Analysis by X‐Ray

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Four Pimarane Diterpenes from Marine Fungus: Chloroform Incorporated in Crystal Lattice for Absolute Configuration Analysis by X-ray

Abstract Separation of the ethyl acetate extract of marine fungus Cryptosphaeria eunomia var. eunomia afforded a new pimarane-type diterpene 1 together with known compounds, 2, 4, and 5, whose absolute configurations were unknown. During recrystallization experiments using chloroform, compounds 1, 2, and 5 gave crystals suitable for X-ray analyses, which revealed that the crystals incorporated chloroform molecules in the crystal lattices. Based on the intense anomalous scattering by chlorine, the absolute configurations of 1, 2, and 5 were unambiguously determined.