Absolute Configuration Of Natural Product Research Articles

Absolute configuration reassignment of nectamazin A: Implications to related neolignans

The ability of nature to produce structurally complex molecules makes the determination of the absolute configuration of natural products a challenging task. Although extensive NMR analysis generally allows for the reliable assignment of relative configurations, the assignments of absolute stereochemistry are commonly performed by empirical comparisons of optical rotation (OR) and/or electronic circular dichroism (ECD) data obtained for related molecules. Such an approach, however, may lead to misassignments and consequent error propagations. Herein, we present the case of the bicyclo(3.2.1)octane neolignan named (+)-nectamazin A. This compound was first reported in 2009 from Nectandra amazonum Nees. (Lauraceae) and had its absolute configuration determined as 7R,8S,3′S,4′R,5′S by means of experimental ECD spectroscopy. Our chemical studies on Ocotea aciphylla (Lauraceae) led to the isolation of (+)-nectamazin A. The extensive analysis of OR, ECD, and vibrational CD data aided by quantum chemical calculations, however, indicated (+)-nectamazin A to have the 7S,8R,3′R,4′S,5′R absolute configuration, in conflict with the configuration reported in the literature. The cause of the original incorrect assignment of (+)-nectamazin A derives from the direct comparison of experimental OR and ECD data obtained for structurally related molecules with different chromophoric systems. As an alternative, VCD spectroscopy is presented as a more reliable and sensitive technique to stereochemical investigations of bicyclo(3.2.1)octane neolignans.

Expanding the Utility of Bioinformatic Data for the Full Stereostructural Assignments of Marinolides A and B, 24- and 26-Membered Macrolactones Produced by a Chemically Exceptional Marine-Derived Bacterium.

Marinolides A and B, two new 24- and 26-membered bacterial macrolactones, were isolated from the marine-derived actinobacterium AJS-327 and their stereostructures initially assigned by bioinformatic data analysis. Macrolactones typically possess complex stereochemistry, the assignments of which have been one of the most difficult undertakings in natural products chemistry, and in most cases, the use of X-ray diffraction methods and total synthesis have been the major methods of assigning their absolute configurations. More recently, however, it has become apparent that the integration of bioinformatic data is growing in utility to assign absolute configurations. Genome mining and bioinformatic analysis identified the 97 kb mld biosynthetic cluster harboring seven type I polyketide synthases. A detailed bioinformatic investigation of the ketoreductase and enoylreductase domains within the multimodular polyketide synthases, coupled with NMR and X-ray diffraction data, allowed for the absolute configurations of marinolides A and B to be determined. While using bioinformatics to assign the relative and absolute configurations of natural products has high potential, this method must be coupled with full NMR-based analysis to both confirm bioinformatic assignments as well as any additional modifications that occur during biosynthesis.

From Relative to Absolute Stereochemistry of Secondary Metabolites: Applications in Plant Chemistry

Structural elucidation of specialized metabolites or natural plant products, especially the stereochemical features of chiral bioactive metabolites, is the most important stage for all investigations in pharmacognosy and phytochemistry. Numerous methods have been established to solve the absolute configuration of natural products, including direct methods such as X-ray diffraction, chiroptical spectroscopy, stereo-controlled partial or total organic synthesis, and chemical correlation by simple organic reactions for derivatization, as well as indirect methods using a standard chiral compound or a derivatizing agent with known absolute configuration, for example, nuclear magnetic resonance by utilization of anisotropic effects of chiral agents. Once the relative configuration of a natural product is resolved, the absolute stereochemistry can be determined with the assistance of chiroptical spectroscopies supported by quantum mechanical-NMR prediction of chemical shifts, scalar coupling constants and simulation of optical rotatory dispersion, in addition to electronic and vibrational circular dichroism spectra. This review summarizes the most practical methods employed in the assignment of absolute stereochemistry of natural plant products with selected examples focused on multichiral center bioactive small molecules from the mega-diverse Brazilian and Mexican flora.

Vibrational Circular Dichroism for the Assignment of Absolute Configuration of Natural Products in Brazil

Vibrational Circular Dichroism for the Assignment of Absolute Configuration of Natural Products in Brazil

The enduring legacy of Koji Nakanishi's research on bioorganic chemistry and natural products. Part 1: Isolation, structure determination and mode of action.

In this brief review on Koji Nakanishi's remarkable career in natural products chemistry, we have highlighted a number of his accomplishments that illustrate the broad diversity of his interests. These include the isolation, structure determination, and biological mechanism of action of many natural products including the triterpenoid pristimerin; the diterpenoid ginkgolides; insect and crustacean molting hormones; phytoalexins; the toxic red tide principle brevetoxin; the vanadium tunicate pigments; philanthotoxin from killer wasps; antisickling agents; mitomycin DNA adducts; insect antifeedants; a mitotic hormone, the small molecule fish attractants from the sea anemone; new isolation and purification technologies; molecular chemistry of vision; age-related macular degeneration; and the development of the exciton circular dichroism (CD) chirality method for microscale determination of absolute configuration of natural products and chirality of other chiral molecules and supramolecular assembly.

Vibrational spectra and theoretical calculations of a natural pentacyclic triterpene alcool isolated from Mucuna pruriens

Nematode control is a significant problem in agriculture industry all over the world. The control is often made with the use of toxic chemicals which can bring detrimental effect to humans, animals, and the environment. Therefore, developing an alternative method of control has become an area of interest such as use of antagonistic plant. Among the variety of antagonist plant species, Mucuna genus are most commonly used. We have carried out a study of the secondary metabolites present on the aerial parts of Mucuna pruriens var. utilis, from which it was isolated and purified a pentacyclic triterpene alcohol, named glutinol. This is the first time the isolation of glutinol is described from this plant species. Identification of this natural product was carried out using infrared, Raman, and NMR spectroscopies. The assignment of the vibrational frequencies was assisted by theoretical calculations using two functionals (HF and B3LYP). Raman optical activity (ROA) frequencies were calculated to assist in te detailed identification of the broad band observed at 2926 cm−1 in the experimental Raman spectrum. The calculated ROA spectra for glutinol (S configuration for the carbon bonded to the hydroxyl group) and R-glutinol (R configuration for the carbon bonded to the hydroxyl group) are discussed to show the potential of this technique to determine the absolute configuration of natural products.

Absolute configuration determination of asarinin by synchrotron radiation with crystalline sponge method

The determination of the absolute configuration of natural products still faces many challenges, especially the active pharmaceutical ingredient which is trace, oily and novel structures. Currently, NMR requires chiral reagents in determining the absolute configuration; ECD involves theoretical calculations and requires chromophores. In this study, the absolute configuration of asarinin had successfully identified by using synchrotron radiation with crystalline sponge method and combining MS with NMR. This method could identifying the crystal structure of trace amorphous substances, resolving the problem of absolute configuration of multi-chiral central compounds, and hopefully providing a new idea and approach for structural elucidation of natural products.

Challenges in the configuration assignment of natural products. A case-selective perspective.

Covering: up to 2018 Even today, when planar structures of natural products can be determined with microgram samples, the configurational assignment continues to be a challenge. The relative and absolute configurations of natural products can be assigned by devising original approaches, relying on carefully acquired data on a case-by-case basis. In this review, the most widely available methods and techniques for the absolute configuration determination of novel natural products are concisely discussed. Selected illustrative examples (case studies) are presented, where original approaches integrating different chemical, spectroscopic, and/or computational methods have been devised to solve intriguing stereochemistry issues of natural small molecules.

Asymmetric Total Synthesis of Andranginine and Absolute Configuration of Natural Product Isolated from Kopsia arborea

Asymmetric Total Synthesis of Andranginine and Absolute Configuration of Natural Product Isolated from Kopsia arborea

Cytotoxic Serrulatane-Type Diterpenoids from the Gorgonian Euplexaura sp. and Their Absolute Configurations by Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) method has become robust and reliable alternative for the stereochemical characterization of natural products. In this paper, three new serrulatane-type diterpenoids, euplexaurenes A–C (1–3), and a known metabolite, anthogorgiene P (4), were obtained from the South China Sea gorgonian Euplexaura sp. GXWZ-05. The absolute configuration of C-11 in 1–4, which was difficult to be determined by common means due to the high conformational flexibility of the eight-carbon aliphatic chain attached at C-4, was determined by VCD method, suggesting a new horizon to define the absolute configurations of natural products possessing chains. Compounds 1–4 were found to show selective cytotoxic activities against human laryngeal carcinoma (Hep-2) cell line with the IC50 values of 1.95, 7.80, 13.6 and 5.85 μM, respectively.

Importance and Difficulties in the Use of Chiroptical Methods to Assign the Absolute Configuration of Natural Products: The Case of Phytotoxic Pyrones and Furanones Produced by Diplodia corticola.

α-Pyrones and furanones are metabolites produced by Diplodia corticola, a pathogen of cork oak. Previously, the absolute configuration (AC) of diplopyrone was defined by chiroptical methods and Mosher's method. Using X-ray and chiroptical methods, the AC of sapinofuranone C was assigned, while that of the (4S,5S)-enantiomer of sapinofuranone B was established by enantioselective total synthesis. Diplofuranone A and diplobifuranylones A-C ACs are still unassigned. Here electronic and vibrational circular dichroism (ECD and VCD) and optical rotatory dispersion (ORD) spectra are reported and compared with density functional theory computations. The AC of the (4S,5S)-enantiomer of sapinofuranone B and sapinofuranone C is checked for completeness. The AC of diplobifuranylones A-C is assigned as (2S,2'S,5'S,6'S), (2S,2'R,5'S,6'R), and (2S,2'S,5'R,6'R), respectively, with the Mosher's method applied to define the absolute configuration of the carbinol stereogenic carbon. The AC assignment of sapinofuranones is problematic: while diplofuranone A is (4S,9R), sapinofuranones B and C are (4S,5S) according to ORD and VCD, but not to ECD. To eliminate these ambiguities, ECD and VCD spectra of a di-p-bromobenzoate derivative of sapinofuranone C are measured and calculated. For phytotoxicity studies, it is relevant that all six compounds share the S configuration for the stereogenic carbon atom of the lactone moiety.

Asymmetric Total Synthesis of Pentacyclic Indole Alkaloid Andranginine and Absolute Configuration of Natural Product Isolated from Kopsia arborea.

The first asymmetric total synthesis of andranginine (1) via an asymmetric Morita-Baylis-Hillman reaction and a diastereoselective intramolecular Diels-Alder reaction has revealed that natural andranginine (1) isolated from Kopsia arborea existed as a scalemic mixture and contained predominantly the (16R,21S) form rather than the (16S,21R) form.

Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products

Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013-2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.

Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products

Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013-2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.

Total synthesis of gobiusxanthin stereoisomers and their application to determination of absolute configurations of natural products: revision of reported absolute configuration of epigobiusxanthin.

(3R)-Gobiusxanthin stereoisomers (1a–d) were synthesized by stereoselective Wittig reaction of the (3R)-C15-acetylenic tri-n-butylphosphonium salt 7 with C25-apocarotenal stereoisomers 5a,b and 14a,b bearing four kinds of 3,6-dihydroxy-ε-end groups. The validity of the reported stereochemistry of gobiusxanthin was demonstrated by the fact that the reported spectral data of natural gobiusxanthin were in agreement with those of synthetic (3R,3'S,6'R)-gobiusxanthin (1a). On the other hand, the reported CD spectral data of natural epigobiusxanthin, which has been assigned as (3R,3'R,6'R)-isomer (3'-epigobiusxanthin), were identical with those of synthetic (3R,3'S,6'S)-isomer 1d (6'-epigobiusxanthin) rather than those of the corresponding synthetic 3'-epi-isomer 1b. It was found that the stereochemistry at C3-position has little effect on the shape of their CD spectra. Thus, in order to reinforce the validity of the absolute configurations at C3-position of natural specimens, (3S,3'S,6'R)- and (3S,3'S,6'S)-stereoisomers 1e and 1f were also synthesized and a HPLC analytical method for four stereoisomers was established by using a column carrying a chiral stationary phase. The HPLC analysis has proven that the stereochemistry of the natural epigobiusxanthin is 3R,3'S,6'S.

Enantiodivergent syntheses of (−)- and (+)-dysibetaine CPa and N-desmethyl analog

The first total syntheses of (−)-dysibetaine CPa and the antipode have been achieved using enantioselective solvolysis of meso-cyclic anhydride mediated by quinine derivative as an organocatalyst. The synthesis features a demonstration of an enantiodivergent organic synthesis of both enantiomers of dysibetaine CPa whereby the absolute configurations of natural product were elucidated as (3R,4R). Application of the present methodology to an enantiomerically pure novel GABA analog is also reported.

Determination of the absolute configuration of natural products

Determination of the absolute configuration of natural products

ChemInform Abstract: Assignment of the Absolute Configurations of Natural Products by Means of Solid‐State Electronic Circular Dichroism and Quantum Mechanical Calculations

AbstractReview: 156 refs.

First enantioselective total synthesis of (−)-dysibetaine CPa and absolute configurations of natural product

Here we report total synthesis of enantiomerically pure dysibetaine CPa, isolated from Micronesian marine sponge and expected to serve as a neuroactive agent. Starting from meso-cyclopropane triester, the synthesis was achieved in 12.8% overall yield over 10 steps including organocatalytic enantioselective solvolysis of meso-succinic anhydride as a key step. This work established the absolute configurations of the natural product as (3R,4R).

Determination of the absolute configuration of natural products

Structural elucidation of natural products is always one of the most important tasks for natural product researchers in related fields. Particularly, the absolute configuration (AC), being a great challenge for natural product chemists, has attracted much attention. During the past few decades, many techniques and approaches have been developed to determine the AC of natural products, including direct (or absolute) methods, e.g. X-ray diffraction (XRD), electronic and vibrational circular dichroism (ECD and VCD), and Raman optical activity (ROA), as well as indirect (or relative) methods using a reference or a derivatizing agent with known AC, e.g. CD with empirical rules and nuclear magnetic resonance (NMR) utilizing anisotropic effects of chiral derivatizing agents. However, none of the currently applied techniques is capable of dominating AC determination, since they each have their respective limitations corresponding to the different structural features. This mini review summarizes most of the techniques and methods which are commonly used in AC assignment of natural products, or have potential application prospects, and briefly describes their principles, advantages and limitations.