Absolute configuration reassignment of two chromanes from Peperomia obtusifolia (Piperaceae) using VCD and DFT calculations

Previous analysis of the ECD spectra of two prenylated benzopyrans isolated from Peperomia obtusifolia, by means of the helicity rule for the chromane chromophore, resulted in the incorrect assignment of their absolute configuration, (S) instead of (R) for a deduced P-helicity of the chromane ring for the (+)-enantiomers. This was discovered by the application of DFT calculations and VCD spectroscopy. Experimental and calculated (B3LYP/6-31G(d)) VCD and IR spectra were compared, and a definitive absolute configuration of (+)-1 and (+)-2 is reassigned directly in solution as (R). The assumption of equatorial positioning of bulky groups, shown here to be invalid for the title molecules, is the underlying cause of the previous incorrect assignment of absolute configuration. Moreover, TDDFT (B3LYP/6-311++G(2d,2p)//B3LYP/6-31G(d)) calculations of ECD spectra have shown that both P- and M-helicity of the heterocyclic ring, for a given absolute configuration, lead to the same sign for the ¹L_b ECD band, thus bringing into question the validity of the empirical ECD helicity rule for chromane molecules.     

Aphagranols D – H: Five New Limonoids from the Fruits of Aphanamixis grandifolia

Five new limonoids, aphagranols D–H ( 1 – 5 , resp.), were isolated from the EtOH extract of the fruits of Aphanamixis grandifolia by chromatographic methods. Their structures were established on the basis of extensive spectroscopic analyses. The absolute configuration of 1 was determined by comparison the experimental and calculated electronic circular dichroism (ECD) spectra. All of the isolates were evaluated for insecticidal activities.     

Determination of absolute configuration using density functional theory calculations of optical rotation and electronic circular dichroism: chiral alkenes

In principle, the absolute configuration (AC) of a chiral molecule can be deduced from its optical rotation (OR) and/or its electronic circular dichroism (ECD). In practice, this requires reliable methodologies for predicting OR and ECD. The recent application of ab initio time-dependent density functional theory (TDDFT) to the calculation of transparent spectral region OR and ECD has greatly enhanced the reliability with which these phenomena can be predicted. TDDFT calculations of OR and ECD are being increasingly utilized in determining ACs. Nevertheless, such calculations are not perfect, and as a result, ACs determined are not 100% reliable. In this paper, we examine the reliability of the TDDFT methods in the case of chiral alkenes. Sodium d line specific rotations, [alpha]D, are predicted for 26 conformationally rigid alkenes of known AC, ranging in size from 5 to 20 C atoms, and with [alpha]D values in the range of 0-500. The mean absolute deviation of predicted [alpha]D values from experimental values is 28.7. With one exception, beta-pinene, the signs of [alpha]D are correctly predicted. Errors in calculated [alpha]D values are approximately random. Our results define a "zone of indeterminacy" within which calculated [alpha]D values cannot be used to determine ACs with >95% confidence. TDDFT ECD spectra are predicted for eight of the alkenes and compared to experimental spectra. Agreement ranges from modestly good to poor, leading to the conclusion that TDDFT calculations of ECD spectra are not yet of sufficient accuracy to routinely provide highly reliable ACs. TDDFT OR calculations for two conformationally flexible alkenes, 3-tert-butylcyclohexene and trans-4-carene, are also reported. For the former, predicted rotations are incorrect in sign over the range 589-365 nm. It is possible that the AC of this molecule has been incorrectly assigned.     

Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra

The enzymatic oxidation of urate leads to the sequential formation of optically active intermediates with unknown stereochemistry: (-)-5-hydroxyisourate (HIU) and (-)-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). In accordance with the observation that a defect in HIU hydrolase causes hepatocarcinoma in mouse, a detoxification role has been proposed for the enzymes accelerating the conversion of HIU and OHCU into optically active (+)-allantoin. The enzymatic products of urate oxidation are normally not present in humans, but are formed in patients treated with urate oxidase. We used time-dependent density functional theory (TDDFT) to compute the electronic circular dichroism (ECD) spectra of the chiral compounds of urate degradation (HIU, OHCU, allantoin) and we compared the results with experimentally measured ECD spectra. The calculated ECD spectra for (S)-HIU and (S)-OHCU reproduced well the experimental spectra obtained through the enzymatic degradation of urate. Less conclusive results were obtained with allantoin, although the computed optical rotations in the transparent region supported the original assignment of the (+)-S configuration. These absolute configuration assignments can facilitate the study of the enzymes involved in urate metabolism and help us to understand the mechanism leading to the toxicity of urate oxidation products.     

Determining the absolute configuration of two marine compounds using vibrational chiroptical spectroscopy

Chiroptical techniques are increasingly employed for assigning the absolute configuration of chiral molecules through comparison of experimental spectra with theoretical predictions. For assignment of natural products, electronic chiroptical spectroscopies such as electronic circular dichroism (ECD) are routinely applied. However, the sensitivity of electronic spectral parameters to experimental conditions and the theoretical methods employed can lead to incorrect assignments. Vibrational chiroptical methods (vibrational circular dichroism, VCD, and Raman optical activity, ROA) provide more reliable assignments, although they, in particular ROA, have been little explored for assignments of natural products. In this study, the ECD, VCD, and ROA chiroptical spectroscopies are evaluated for the assignment of the absolute configuration of a highly flexible natural compound with two stereocenters and an asymmetrically substituted double bond, the marine antibiotic Synoxazolidinone A (SynOxA), recently isolated from the sub-Arctic ascidian Synoicum pulmonaria. Conformationally averaged nuclear magnetic resonance (NMR), ECD, Raman, ROA, infrared (IR) and VCD spectral parameters are computed for the eight possible stereoisomers of SynOxA and compared to experimental results. In contrast to previously reported results, the stereochemical assignment of SynOxA based on ECD spectral bands is found to be unreliable. On the other hand, ROA spectra allow for a reliable determination of the configuration at the double bond and the ring stereocenter. However, ROA is not able to resolve the chlorine-substituted stereogenic center on the guanidinium side chain of SynOxA. Application of the third chiroptical method, VCD, indicates unique spectral features for all eight SynOxA isomers in the theoretical spectra. Although the experimental VCD is weak and restricted by the limited amount of sample, it allows for a tentative assignment of the elusive chlorine-substituted stereocenter. VCD chiroptical analysis of a SynOxA derivative with three stereocenters, SynOxC, results in the same absolute configuration as for SynOxA. Despite the experimental challenges, the results convincingly prove that the assignment of absolute configuration based on vibrational chiroptical methods is more reliable than for ECD.     

Absolute configuration of conformationally flexible cis-dihydrodiol metabolites by the method of confrontation of experimental and calculated electronic CD spectra and optical rotations

We have determined the absolute configurations of conformationally flexible cis-dihydrodiol metabolites (cis-1,2-dihydroxy-3,5-cyclohexadienes), bearing different substituents (e.g., Br, F, CF3, CN, Me) in 3- and 5-positions, by the method of confrontation of experimental and calculated electronic CD spectra and optical rotations. Convergent results were obtained by both methods in eight out of ten cases. For the difficult cases, where either conformer population and/or chiroptical properties (calculated rotational strengths of the long-wavelength Cotton effect or optical rotations) of contributing conformers remain inconclusive, the absolute configuration could still be correctly assigned based on one of the biased properties (either ECD or optical rotation). This approach appears well-suited for a broad spectrum of conformationally flexible chiral molecules.     

Palmarumycins from the Endophytic Fungus Lasiodiplodia pseudotheobromae XSZ‐3

One new and three known spiro‐dioxynaphthalene compounds, related to palmarumycins, were isolated from the extracts of fungus Lasiodiplodia pseudotheobromae XSZ‐3. Their structures were established by spectroscopic methods (1D‐ and 2D‐NMR, HR‐ESI‐MS, etc.). The absolute configuration of 1 was determined by comparison of quantum‐chemical TDDFT (time‐dependent density‐functional theory) calculated and experimental ECD (electronic circular dichroism) spectra. The cytotoxic activities of 1 – 4 against HL‐60 cell line were evaluated by trypan blue‐staining assay.     

Theoretical calculation of electronic circular dichroism of the rotationally restricted 3,8'-biflavonoid morelloflavone

Theoretical calculation of electronic circular dichroism (ECD) of the rotationally restricted 3,8'-biflavonoid (+)-morelloflavone using time dependent density functional theory (TDDFT), performed at 298 K at B3LYP-SCRF/6-31G*//B3LYP/6-31G* level with COSMO model, permitted unequivocal assignment of its 2R,3S absolute configuration. The experimentally observed Cotton effect (CE) around 290 nm is contributed by the acetophenone pi --> pi* transition of the ABC-flavanone moiety and the electronic transition within the DEF-flavone moiety, while another diagnostic positive CE around 350 nm is attributable to the electronic interaction between the ABC-flavanone moiety and the DEF-flavone moiety, as well as the electronic transition within the DEF-flavone moiety. The remarkable differences of the calculated ECD of its two rotamers indicate that the rotational restrictions significantly affect the ECD of 3,8'-biflavonoids. Empirical ECD rules derived from monomeric flavonoids may not be applicable to configurational assignment of complex 3,8'-biflavonoids. This study has provided new insights in interpreting the experimentally observed ECD spectra of this class of compounds.     

Assignment of Absolute Configuration of Bromoallenes by Vacuum-Ultraviolet Circular Dichroism (VUVCD)

A new application of vacuum-ultraviolet circular dichroism (VUVCD), which enables the measurement of CD spectra in the vacuum-ultraviolet region (140–200 nm), for the assignment of the absolute configurations of bromoallenes is described. Bromoallene moieties are found in natural products obtained from many marine organisms. To date, the absolute configuration of bromoallenes has been assigned almost exclusively with Lowe’s rule, which is based on specific rotation. However, exceptions to Lowe’s rule have been reported arising from the presence of other substituents with large specific rotations. For the unambiguous assignment of the absolute configuration of the bromoallene moiety with its characteristic absorption wavelength at 180–190 nm due to the π–π* transition, VUVCD was applied to four pairs of bromoallene diastereomers prepared by modifying the synthetic scheme of omaezallene. The VUVCD spectra clearly showed positive or negative Cotton effects around 180–190 nm according to the configuration of the bromoallene employed, revealing the potential of VUVCD for determining absolute stereochemistry.     

Absolute configuration of C76 from optical rotatory dispersion.

The absolute configuration of C76 has been determined as (+)589-(fC)-C76 , for the first time, by comparing the experimental and predicted optical rotatory dispersion (ORD) patterns. The experimental ORD pattern was derived from the experimental electronic circular dichroism (ECD) spectrum using the Kramers-Kronig (KK) transform. The theoretical ORD spectra were calculated in the resonant region using linear response theory, and also using the KK transform of the theoretical ECD spectrum, at different theoretical levels, namely BHLYP/6-31G*, B3LYP/6-31G*, BLYP/6-31G*, and HF/6-31G*. Good agreement noted between experimental and predicted spectra allows for an unambiguous determination of the absolute configuration.     

Structure and absolute configuration of hydroxy‐bis‐dihydrofarinosin from Encelia farinosa

The structure of the dimeric eudesmanolide hydroxy‐bis‐dihydrofarinosin ( 1 ) from Encelia farinosa followed after contrasting their ¹H and ¹³C NMR spectra with those of encelin ( 6 ), hydroxy‐bis‐dihydroencelin ( 3 ), and farinosin ( 4 ). Structure  1 was verified by single‐crystal X‐ray diffraction analysis, which further provided the stereochemistry of the hydroxy group at C‐4. Comparison of the experimental vibrational circular dichroism spectrum of its derived diacetate 2 with that calculated by density functional theory provided the absolute configuration, which resulted the same as that of its biogenetic precursor 4 . Evaluation of several chemical shift differences between the two eudesmanolide fragments of 1 and 3 allows also ascertaining the yet not reported absolute configuration of the C‐4 stereogenic center of 3 . Copyright © 2016 John Wiley & Sons, Ltd.     

Discussion of absolute configuration for bioactive Griseusins by comparing computed optical rotations and electronic circular dichroism with the experimental results

Absolute configurations of seven bioactive natural Griseusins were investigated. Optical rotation and electronic circular dichroism were calculated at the B3LYP/6-311++G(2d,p)//PCM/B3LYP/6-311++G(2d,p) or other levels in the gas phase and/or in solution. Computational results exhibited that the early reported absolute configuration of four among the seven may not be the best structures after comparing the computed optical rotations, electron circular dichroisms to the experimental data. Then four favorable structures are suggested based on the comparison of predicted optical rotations and electronic circular dichroisms to the experimental results. It is the first time to find that the different position of carbonyl group on aromatic ring (planar structure changes) in Griseusins can lead to the ECD curve reversed instead of the stereogenic center changes. In traditional opinion, ECD curve reversal happens only when stereogenic center configuration reverses, such as from AC of (R) to (S).     

Tribenzotriquinacenes Based on Regioselective Bis‐formylation: Optical Resolution and Absolute Configuration of Inherently Chiral Derivatives and Synthesis of the First Cyclophane‐Type Tribenzotriquinacene Dimers

Enantiomerically pure tribenzotriquinacenes (TBTQs) bearing two monofunctionalized aromatic nuclei were synthesized for the first time and their optical properties and absolute configuration determined. A remarkably regioselective bis‐formylation of the fully bridgehead methylated parent TBTQ hydrocarbon with MeOCHCl₂/TiCl₄ afforded a mixture of two C_s‐symmetrical (achiral) difunctionalized derivatives together with one C₁‐symmetrical (chiral) isomer. Reduction and subsequent column chromatography furnished the three respective benzylic TBTQ dialcohols. Optical resolution of the racemic 2,6‐bis(hydroxymethyl) derivative was achieved via the diastereomeric (R)‐1,1′‐bi‐2‐naphthol ethers and the absolute configuration of the enantiomers was determined by CD exciton model analysis. The electronic circular dichroism (ECD) spectra and the specific rotation of the enantiomers were found to agree with the results of DFT calculations. Among the C_s‐symmetrical isomers, the “proximal” 2,11‐dialdehyde and the corresponding benzylic dialcohol were identified by 2D NMR spectroscopy and X‐ray crystallographic analysis, respectively, and used as the starting point for the synthesis of several novel dithiametacyclophanes. These include the first “dimeric” tribenzotriquinacene‐based cyclophanes bearing the bowls of the two TBTQ units attached to each other in a syn (concave–concave) or anti (convex–concave) configuration. The usefulness of such thiacyclophanes as fluorescent chemosensors for different metal ions is also demonstrated.     

Synthesis of the Natural Product Building Block 5‐(3‐Bromophenyl)‐4‐hydroxy‐5‐methylhexan‐2‐one and its Chiral Characterization by Using Chiroptical Spectroscopy

The absolute configuration of 5‐(3‐bromophenyl)‐4‐hydroxy‐5‐methylhexan‐2‐one, an intermediate in the synthesis of various natural products, is assigned by using vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and optical rotatory dispersion (ORD). Experimental spectra were compared to density functional theory (DFT) calculations of the molecule with known configuration. These three techniques independently confirm that the absolute configuration is (S)‐5‐(3‐bromophenyl)‐4‐hydroxy‐5‐methylhexan‐2‐one, thus enabling us to assign the absolute configuration with high reliability. The reliability of the VCD analysis was assessed quantitatively by using the CompareVOA program. We found that, in cases in which the agreement between theory and experiment was very good, a value of 10 cm^?1 for the triangular weighting function gave a more‐realistic discriminative power between enantiomers than the default value of 20 cm^?1.     

Stereochemical differentiation of C‐7 hydroxyltaxane isomers by electrospray ionization mass spectrometry

In this study, different electrospray ionization mass spectrometric (ESI‐MS) methods were utilized to analyze several pairs of taxane stereoisomers including paclitaxel and 7‐epi‐paclitaxel. Both ESI‐MS and tandem mass spectrometry (MS/MS) techniques provided stereochemically dependent mass spectra in negative‐ion mode, and all studied stereoisomers could be easily distinguished based on their characteristic ions or distinct fragmentation patterns. MS/MS experiments for several taxane analogues at various collision energies were performed to elucidate potential dissociation pathways. The gas‐phase deprotonation potentials were also calculated to estimate the most thermodynamically favorable deprotonation site using DFT B3LYP/6‐31G(d). The results of the theoretical studies agreed well with the fragmentation patterns of paclitaxel and 7‐epi‐paclitaxel observed from MS/MS experiments. In addition, it was found that liquid chromatography (LC)/ESI‐MS was a useful and sensitive technique for assignment of C‐7 taxane stereoisomers from realistic samples. Copyright © 2009 John Wiley & Sons, Ltd.     

Time‐dependent density functional theory calculations on the chiroptical properties of rubroflavin: Determination of its absolute configuration by comparison of measured and calculated CD spectra

The absolute configuration of rubroflavin has been determined by comparison of its measured and calculated CD spectra. For this purpose the structures of 30 plausible isomers of the title compound have been optimized with density functional theory (DFT/BP86) using a triple‐zeta valence basis set. The absolute (S) configuration at the ? S(?O)CH₃ group has been assumed in these calculations. One quinoid isomer, which is separated from all other structures by an energy gap of about 4 kcal/mol, was found to be the most stable species and to dominate the CD spectrum. The structure of this isomer has been reoptimized under the influence of a solvent using an electrostatic model (COSMO). Based on the geometries of the most stable isomer obtained in the presence and absence of the solvent the excitation energies and oscillator as well as rotational strengths have then been calculated using time‐dependent DFT (TDDFT/TZVP/BP86). Comparison of the measured CD spectrum with that calculated for the energetically lowest isomer shows that especially the long wavelength parts of the spectra agree fairly well as far as the wavelengths and the signs of the Cotton effects are concerned while the correspondence between calculated and measured intensities is less satisfying. The agreement between the measured and calculated spectrum is better if the geometry optimized under the influence of the solvent is used. A detailed analysis of the spectra led us to the conclusion that the absolute configuration of rubroflavin is (S). These results support earlier assignments based on semiempirical and ab initio studies on a thermal decomposition product of rubroflavin. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 265–270, 2003     

A single chiroptical spectroscopic method may not be able to establish the absolute configurations of diastereomers: dimethylesters of hibiscus and garcinia acids

Electronic circular dichroism (ECD), optical rotatory dispersion (ORD), and vibrational circular dichroism (VCD) spectra of hibiscus acid dimethyl ester have been measured and analyzed in combination with quantum chemical calculations of corresponding spectra. These results, along with those reported previously for garcinia acid dimethyl ester, reveal that none of these three (ECD, ORD, or VCD) spectroscopic methods, in isolation, can unequivocally establish the absolute configurations of diastereomers. This deficiency is eliminated when a combined spectral analysis of either ECD and VCD or ORD and VCD methods is used. It is also found that the ambiguities in the assignment of absolute configurations of diastereomers may also be overcome when unpolarized vibrational absorption is included in the spectral analysis.     

Citriperazines A-D produced by a marine algae-derived fungus Penicillium sp. KMM 4672

Abstract

Four new diketopiperazine alkaloids, citriperazines A-D were isolated from algae-derived Penicillium sp. KMM 4672. The structures of compounds 1–4 were determined using spectroscopic methods. The absolute configurations of compounds 1 and 4 were established by comparison of calculated and experimental ECD spectra. The cytotoxicity of compounds 1–4 against several human prostate cell lines was evaluated.     

Taxane Diterpenoids from the Root Bark of Taiwanese Yew Taxus Mairei

Nineteen compounds including taxumairol R (1) , taxinine M (2) , taxacin (3) , paclitaxel (4) , 10‐deacetyltaxol A (5) , 10‐deacetyl‐7‐epi‐taxol (6) , 7‐epi‐taxol (7) , taxol C, 10‐deacetyltaxol C, 7β‐xylosyl‐10‐deacetyltaxol (8) , taxamairin A (9) , taxinine A, 14β‐hydroxytaxusin (10) , 5α‐hydroxy‐7β,9α,10β, 13α‐tetraacetoxy‐4(20), 11‐taxadiene, 1‐dehydroxybaccatin‐VI, 1β‐dehydroxybaccatin‐IV, baccatin IV, baccatin VI and ponasterone A have been isolated and identified from the root bark of Taxus mairei. Among them, compound 1 was a new taxoid and compounds 11 and 7β‐xylosyl‐10‐deacetyltaxol pentaacetate were new derivatives prepared from 14β‐hydroxytaxusin (10) and 8 , respectively. Their structures and assignment were established on the basis of 2D‐NMR analysis and chemical methods.