Pedro Joseph-Nathan

Introduction: The ¹³C-NMR data described for perezone (1), a 3-hydroxy p-quinone stated as the first natural product isolated as crystals in the New World, and rigidone (2), a 4-hydroxy o-quinone isolated from a coral species, are essentially the same. Some years ago, we described, using theoretical calculations, that a 4-hydroxy-1,2-quinone is more than 11 kcal/mol less stable than a 3-hydroxy-1,4-quinone making coexistence in nature of this type of quinones. In the present study, we approach the situation by comparing of the experimental ¹³C-NMR data for 1 and those described for 2 with the calculated using computational methods. Additional evidence was obtained from a X-ray diffraction analysis for the reaction product of perezone with o-phenylendiamine. Methods: The ¹³C-NMR data for the quinoid rings were calculated using the GIAO and CSGT methods, density functional theory (DFT) and the functional/basis set pairs B3LYP/6-31 g(d,p) and MPW1PW91/6-31 g(d,p); and TPSSTPSS/cc-PVTZ and PBE1PBE/aug-cc-PVDZ. Perezone reaction with o-phenylenediamine was achieved using a described method in MeOH at room temperature. X-Ray diffraction analysis of phenazine from perezone reaction was done using Mo Kα radiation. The data were used to calculate the Flack parameter. Results: After conformational analysis, complete optimization of the geometry of the conformers found and, calculation of the ¹³C-NMR chemical shifts for the quinone ring of 1 and 2, in all cases a better agreement was observed between the experimental data for 1 versus 2. Perezone reaction with o-phenylenediamine afforded the corresponding phenazine in its amine-keto tautomeric form as evidenced from a X-ray diffraction study. Conclusion: The better agreement observed between the experimental and calculated data for 1 versus 2, along with the free energy difference of more than 11 kcal/mol in favor of the 3-hydroxy p-quinone versus 4-hydroxy o-quinone, previously established for us, allow to say that the structure described for rigidone corresponds to ent -perezone.

Diosgenin (1a) is used as a raw starting material for the synthesis of steroid hormones and contraceptives and is probably one of the most commercially important steroidal sapogenins. The literature on 1a is extensive, and topics range from its isolation from a variety of natural sources to its chemical modifications and therapeutic properties as an anti-cancer, anti-diabetic, anti-thrombosis, anti-inflammatory, and anti-viral agent, among others. ¹ The spectroscopic characteristics of 1a have been analyzed for a long time, but the assignment of the complete ¹H NMR profile remains incomplete due to the overlapping signals obtained with the most common spectrometers. In the current study, the 750-MHz ¹H NMR spectrum of diosgenin benzoate (1b) has been completely assigned by means of QM-based ¹H iterative full spin analysis (HiFSA), which is used for the complete ¹H NMR description of intricate natural products and the quality control of pharmaceuticals. ² The complete assignment was facilitated by taking advantage of some chemical shifts described for 1a and the coupling constants of the cholestane skeleton of cholesteryl benzoate, which were also recently calculated by HiFSA. ³

Inverse epimers are uncommon in nature and a lack of study of their vibrational circular dichroism (VCD) behavior seems evident. This is relevant, among other facts, since in the case of epimers, VCD has been capable of determining the absolute configuration (AC) of 1 stereogenic center in a molecule having 10 stereogenic centers. The case of pipitzol is unique since it took 80 years from its first preparation by thermal intramolecular cycloaddition of perezone (1) to know that the reaction outcome is an equimolar mixture of the 2 inverse epimers α-pipitzol (2: 3 R, 3a R, 7 R, and 8a S) and β-pipitzol (3: 3 R, 3a S, 7 S, and 8a R). Evaluation of 2 and 3 reveals that some VCD bands have an opposite phase while other bands show the same phase. The VCD spectrum of the naturally occurring equimolecular mixture was also measured and the 3 experimental spectra were contrasted with density functional theory (DFT) calculated spectra allowing individual band assignments. The comparisons were made in the 1800 to 950 and 1550 to 950 cm⁻¹ ranges and the numerical differences are highlighted thereby showing that carbonyl bands influence such comparisons. The 2 carbonyl absorption bands of 2 and 3 show weak VCD bands and the conjugated double bond band provides an intense AC-dependent VCD band.

The aerial parts ofAgeratina vernalisprovided the new germacranolide 1,10-epoxydeltoidin A (3), together with the known pentacyclic triterpenoid hopane-6 alpha,22-diol (1), and the also known germacranolides deltoidin A (2) and 15-hydroxydeltoidin A (4). In addition,pTsOH catalyzed cyclization of2afforded the new guaianolide5. The absolute configuration of2,4, and5was assigned by vibrational circular dichroism spectroscopy, while the complete(1)H and(13)C NMR data assignments of2-5followed from 1 D- and 2 D-NMR experiments.

Although tremetone [5-acetyl-2-(1-methylvinyl)-2,3-dihydrobenzofuran] has only one stereogenic center, the absolute configuration (AC) determination of its naturally occurring 11-acyloxy derivatives 1 and 2 by vibrational circular dichroism (VCD) turned out to be difficult. Similarity-based comparison of the experimental VCD spectrum of 11-coumaryloxytremetone (1), isolated from Parastrephia quadrangularis, with spectra calculated using popular density functional theory (DFT) levels of theory, provided poor enantiomeric similarity indices ( ESI), even when the p-coumaroyl ester group of 1 was replaced by the acetyl group in 2. In search for a better understanding of these results, IR-guided individual scaling factors (ISFs), recently introduced as part of the Vibrational Spectra Similarity and Analysis Tool (VISSAT) software, were used to correct DFT frequencies, while a VCD-guided conformational analysis was developed to explore conformational preferences. These studies showed that for both molecules 72% of the individual conformations gave ESI values in favor of the ( R) enantiomer. Likewise, when conformer abundances were optimized to produce the best possible similarity for each enantiomer, the obtained ESI values were always larger for the ( R) isomer than for the ( S) isomer. These results point toward the ( R) AC in both compounds and highlight the incorrect conformer abundance prediction by DFT calculations as the potential source of the initial difficulties. In addition, the AC of 1 was independently verified using the Flack and Hooft parameters gained after a single-crystal x-ray diffraction (XRD) study.

The occurrence of racemic and enantiomerically enriched (scalemic) mixtures of secondary metabolites in their natural sources is a rare phenomenon. The unprecedent case of enantiomeric variations from levorotatory to dextrorotatory, and back to levorotatory, passing through an almost racemic mixture, was recently documented for areolal, the major epoxythymol of Piptothrix areolare. In an attempt to shed some light to understand the reasons for such an unusual behavior, herein, we evaluated this phenomenon by correlating the areolal enantiomeric purity with several environmental variables, including temperature, humidity, rain precipitation, wind speed, and radiation during over 1 year of the plant life cycle. The specific rotation and enantiomeric excess determined by ¹H‐NMR‐BINOL measurements provided the scalemic variations of areolal samples isolated from the roots collected from the same location along a 427‐day period. The ¹H‐NMR‐BINOL methodology provided better sensitivity to enantiomeric variations than specific rotation measurements. Statistical data, including matrix correlation analysis, exploratory analysis by heatmap plotting, and the principal component analysis (PCA), suggested direct correlation of the scalemic variation with humidity, rain precipitation, and radiation variables with the best PCA explanation (78.4%) and noncritical or poor correlations in PCA explained in 60.2% and 48.4%, respectively. When variations in the optical activity parameter of any metabolite are observed, the search for scalemic mixtures along their host plant life cycle should be undertaken. Herein, this phenomenon could be associated with interactions with soil microorganisms and with evolutionary aspects of Piptothrix areolare which belongs to Asteraceae, one of the most successfully adaptable plant families.

The use of IR individual scaling factors (ISF) for the correction of DFT-calculated frequencies, and its effect on IR and VCD similarity functions, has been evaluated using (+)-(R)-3-methylcyclopentanone as a probe molecule. Contrary to using a single scaling factor to improve spectra matching, this approach sequentially searches for the optimal scaling factor for each calculated transition using a computational search algorithm to maximize the overlap of the calculated and observed IR spectra expressed as the IR similarity (S_IR) function. The obtained ISFs are then applied to the calculated frequencies, which are used to produce a scaled VCD spectrum for comparison with the observed trace, thereby yielding enantiomeric similarity index (ESI) values as a similarity measure. This procedure provides a significant improvement of the S_IR and ESI values when compared with the use of a single scale factor, showing 15.1% and 34.1% in average increments, respectively, and values as high as 0.98 and 0.94, respectively. When a set of manually found ISFs is used, most differences in S_IR and ESI performance disappear, and nearly perfect spectra matches are found throughout the levels of theory tested. This suggests that the observed differences in computed IR/VCD spectra with commonly used levels of theory are related to differences in frequency rather than to intensity accuracy. Finally, the use of ISFs is expected to enhance the ability to aide stereochemical assignments, particularly in cases where sufficiently accurate frequencies are difficult to obtain due to the system size or complexity.

Diastereoisomeric stigmasterol oxiranes 4, 5, 8, and 9 are known phytosterol oxidation products (POPs) that have been evaluated for their cytotoxicity, although the results are of limited significance since, in most cases, they were evaluated as mixtures. Consequently, to establish biological activity hierarchy of these oxides, it is critical to evaluate individual pure POPs. Therefore, we now describe the obtention of individual molecules and their absolute configuration (AC) determination. The two acetylated C‐5−C‐6 oxiranes 6 and 7; the two acetylated C‐22−C‐23 oxides 10 and 11, obtained by means of Δ⁵ double bond protection‐deprotection; and the four C‐5−C‐6, C‐22−C‐23 diepoxystigmasteryl acetates 19–22 were now individually gained and their AC determined by vibrational circular dichroism. Vibrational modes associated with the C‐5−C‐6 and the C‐22−C‐23 bonds were identified in dioxiranes 19–22 and used to assign the AC of monoepoxides 6, 7, 10, and 11. The AC of biological active non‐acetylated molecules follows immediately. Due to the scarce spectroscopic information available for these POPs, the ¹H and ¹³C NMR chemical shifts of 3–22 were assigned using 1D‐ and 2D‐NMR experiments.

The partial or total hydrolysis of (3R,4S,5S,6S,9R,10R,11R)-9,13-diangeloyloxylongipinan-1-one (1), isolated from the roots of Stevia viscida, gave alcohols 2 or 3, respectively, which were subjected to molecular rearrangements with boron trifluoride etherate. Compound 2 afforded (3R,4R,5R,6S,9R,10S,11S)-11,13-oxyneomorelian-1-one (10) and (4S,5R,6S,8S,10R)-10,13-oxyneojiquilp-2-en-1-one (11), both possessing novel sesquiterpenoid skeletons. In turn, 3 provided (3R,4R,5S,6S,9R,11R)-13-hydroxymoreli-10(14)-en-1-one (7) and 10. Acetylation of 3 gave 4, thus allowing reduction of the C-1 carbonyl group to yield 5, which was rearranged to (1S,3R,4S,5S,6S,9R,10R,11R)-13-acetoxy-9,11-epoxyjiquilpane (6), while an attempt to mesylate 3 directly gave rearranged (3R,4R,5S,6S,9R,11R)-13-mesyloxymoreli-10(14)-en-1-one (8) through expulsion of the C-9 mesylate group by the antiperiplanar C-4–C-10 bond migration to C-4–C-9. In addition, treatment of 1 with boron trifluoride etherate generated (3R,4R,5S,6S,9R,11R)-13-angeloyloxymoreli-10(14)-en-1-one (9). The structures of 2–11 were elucidated by 1D and 2D NMR experiments and those of 2, 3, 8, 10, and 11 were confirmed by single-crystal X-ray diffraction analysis.

Since epoxythymols occur in Nature either as scalemic mixtures or as pure enantiomers, the knowledge of their chiral composition and of the absolute configuration (AC) of the dominant enantiomer turns out to be mandatory. This task has already been faced using 1,1-bis-2-naphthol (BINOL), as a chiral solvating agent in accurate ¹H NMR quantifications to determine the enantiomeric ratio, and vibrational circular dichroism (VCD) to evidence the AC of the dominant enantiomer. We now explore the use of electronic circular dichroism (ECD) to determine the AC of an epoxythymol for which time-expensive DFT calculations would be required unless the AC of a related molecule is already known, from either VCD studies or single-crystal X-ray diffraction analysis, since one could correlate the ECD Cotton effect with the AC because in ECD only chromophores and their neighborhoods are evidenced. This method is now applied by using the epoxythymols from Piptothrix areolare. Known areolal (1) and 10-cinnamoyloxy-8,9-epoxythymol isobutyrate (2) were isolated from the roots, while known 7-acetoxy-10-cinnamoyloxy-8,9-epoxythymol isobutyrate (3) and 10-cinnamoyloxy-7-hydroxy-8,9-epoxythymol isobutyrate (4), as well as the new enantiopure 7-acetoxy-10-cinnamoyloxy-6-hydroxy-8,9-epoxythymol isobutyrate (5) and 10-cinnamoyloxy-8,9-epoxy-6-hydroxy-7-northymol isobutyrate (6), were obtained from the extract of the flowers. Chemical correlation of epoxythymols 1 and 3 was achieved. Compounds 1–4 were obtained as scalemic mixtures, and 5 and 6 as the pure (8S) enantiomers. In addition, the new 10-cinnamoyloxy-7-oxo-8,9-dehydrothymol isobutyrate (7) was isolated from the roots. The structures of 5–7 followed from NMR and HRMS data, while enantiomeric compositions of 1–6 were determined by ¹H NMR-BINOL measurements. The AC determination for 2–6 was done by ECD using a sample of 1 to reference the ECD Cotton effect. In turn, the AC of 1 was determined by VCD and extensive DFT calculations. The ECD-BINOL methodology turned out to be some 500 times more sensitive than that combining VCD and ¹H NMR-BINOL.