Stereochemical Assignment Research Articles

Enantioselective synthesis of the aglycone of burnettramic acid A.

Enantioselective total synthesis of the aglycone of burnettramic acid A, an antifungal pyrrolizidinedione with a terminally mannosylated long acyl chain produced by Aspergillus fungi, has been achieved from a known carboxylic acid by a 14-step sequence. The key steps include 2 types of asymmetric alkylation, coupling of an acetylide intermediate with (S)-epichlorohydrin to provide an acetylenic epoxide in 1 pot, and the Birch reduction to effect desulfonylation, semi-reduction of triple bond, and debenzylation in a concurrent manner. Good agreement of the synthetic aglycone with naturally occurring one in 1H and 13C nuclear magnetic resonance (NMR) spectra, coupled with previously reported unambiguous stereochemical assignment of the sugar moiety, has confirmed the structure of burnettramic acid A.

Synthesis of the C28-C41 Side Chain of (Proposed) Neaumycin B: AContiguous Stereohextet.

The C28-C41 side-chain of the proposed structure of neaumycin B, which encompasses a contiguous stereohextet, is prepared in 8 steps (longest linear sequence). Convergency is maximized via Williams' Felkin-Anh-selective triorganozincate-mediated vinylation of an α,β-stereogenic aldehyde. The relative stereochemical assignment of the C33-C35 stereotriad was accomplished via the 13C NMR analysis of the related acetonide. Relative stereochemistry of C33 carbinol and C36-C37 glycidol was determined by comparative NOE analysis of the related diastereomeric furans.

Structurally Diverse Cytotoxic Polyphenols from Garcinia gracilis.

Thirty-five diverse polyphenols, belonging to seven structure classes, were isolated from Garcinia gracilis, a medicinal and edible plant sampled from Laos. The structures of nine new compounds, gargarcilones A-I (1-3, 5-7, 10, 12, and 17), were established using spectroscopic, X-ray diffraction, and experimental and calculated ECD methods. Additionally, we revised the stereochemical assignment of cochinchinoxanthone and cochinchinoxanthone C. The compounds were evaluated for antiproliferative activity against five human tumor cell lines (HL-60, A549, SMMC-7721, MDA-MB-231, and SW480). Compounds 1-4, 7, and 8 exhibited cytotoxic activity with IC50 values of 0.5-8.9 μM. Compound 3 significantly induced apoptosis in SMMC-7721 cells.

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.

Absolute configuration assignment of marine natural products in Brazil

Brazil is one of the most biodiverse countries in the world, with a coastline that stretches over 7,000 km including various marine ecosystems, such as coral reefs, mangroves, and seagrass beds, among other habitats. These diverse environments provide a rich source of compounds, derived from primary or secondary metabolism, which may have countless biological activities. Research on marine natural products (MNP) in Brazil has been ongoing for several decades and led to the discovery of numerous bioactive compounds with potential applications in medicine, agriculture, and cosmetics. These MNP are structurally complex, both from an architectural and stereochemical point of view. However, even with all the well-established techniques for the absolute configuration (AC) assignment, this stage of structural characterization of natural products is still under-explored and remains a challenge. This review presents an overview of natural product chemistry in Brazil, focusing on the stereochemical assignment of marine chiral compounds. The main goals are to describe the techniques employed in the assignments as well as to highlight the importance of choosing the appropriate methods for chiral natural products AC determinations.

Natural-Product-Inspired Microwave-Assisted Synthesis of Novel Spirooxindoles as Antileishmanial Agents: Synthesis, Stereochemical Assignment, Bioevaluation, SAR, and Molecular Docking Studies.

Leishmaniasis is a neglected tropical disease, and there is an emerging need for the development of effective drugs to treat it. To identify novel compounds with antileishmanial properties, a novel series of functionalized spiro[indoline-3,2'-pyrrolidin]-2-one/spiro[indoline-3,3'-pyrrolizin]-2-one 23a-f, 24a-f, and 25a-g were prepared from natural-product-inspired pharmaceutically privileged bioactive sub-structures, i.e., isatins 20a-h, various substituted chalcones 21a-f, and 22a-c amino acids, via 1,3-dipolar cycloaddition reactions in MeOH at 80 °C using a microwave-assisted approach. Compared to traditional methods, microwave-assisted synthesis produces higher yields and better quality, and it takes less time. We report here the in vitro antileishmanial activity against Leishmania donovani and SAR studies. The analogues 24a, 24e, 24f, and 25d were found to be the most active compounds of the series and showed IC50 values of 2.43 µM, 0.96 µM, 1.62 µM, and 3.55 µM, respectively, compared to the standard reference drug Amphotericin B (IC50 = 0.060 µM). All compounds were assessed for Leishmania DNA topoisomerase type IB inhibition activity using the standard drug Camptothecin, and 24a, 24e, 24f, and 25d showed potential results. In order to further validate the experimental results and gain a deeper understanding of the binding manner of such compounds, molecular docking studies were also performed. The stereochemistry of the novel functionalized spirooxindole derivatives was confirmed by single-crystal X-ray crystallography studies.

Breaking the DFT Energy Bias Caused by Intramolecular Hydrogen-Bonding Interactions with MESSI, a Structural Elucidation Method Inspired by Wisdom of the Crowd Theory.

The use of quantum-based NMR methods to complement and guide the connectivity and stereochemical assignment of natural and unnatural products has grown enormously. One of the unsolved problems is related to the improper calculation of the conformational landscape of flexible molecules that have functional groups capable of generating a complex network of intramolecular H-bonding (IHB) interactions. Here we present MESSI (Multi-Ensemble Strategy for Structural Identification), a method inspired by the wisdom of the crowd theory that breaks with the traditional mono-ensemble approach. By including independent mappings of selected artificially manipulated ensembles, MESSI greatly improves the sense of the assignment by neutralizing potential energy biases.

Elucidating Structures of Complex Organic Compounds Using a Machine Learning Model Based on the 13C NMR Chemical Shifts

We present a protocol that combines the support vector machine (SVM) model with accurate 13C chemical shift calculations at the xOPBE/6-311+G(2d,p) level of theory, denoted as SVM-M (i.e., SVM for magnetic property). We show here that this SVM-M protocol is a versatile tool for identifying the structural and stereochemical assignment of complex organic compounds with high confidence. Of particular significance is that, by utilizing the dual role of the decision values in SVM, the present SVM-M protocol provides an accurate yet efficient solution to simultaneously handle the classification issue (i.e., “is a given structure correct or incorrect?”) and the comparison-based problem (i.e., “which structure is more likely to be correct or wrong among several candidate structures?”). A significantly high success rate has been reached (i.e., ∼100% on a set of 760 sample molecules with 15928 13C chemical shifts), which makes the SVM-M protocol a powerful tool for routine applications in structural and stereochemical assignments, as well as in detecting mis-assignments, for complex organic compounds, including natural products.

Revisiting the bromination of 3β-hydroxycholest-5-ene with CBr4/PPh3 and the subsequent azidolysis of the resulting bromide, disparity in stereochemical behavior.

Cholesterol reacts under Appel conditions (CBr4/PPh3) to give 3,5-cholestadiene (elimination) and 3β-bromocholest-5-ene (substitution with retention of configuration). Thus, the bromination of cholesterol deviates from the stereochemistry of the standard Appel mechanism due to participation of the Δ5 π-electrons. In contrast, the subsequent azidolysis (NaN3/DMF) of 3β-bromocholest-5-ene proceeds predominantly by Walden inversion (SN2) affording 3α-azidocholest-5-ene. The structures of all relevant products were revealed by X-ray single crystal structure analyses, and the NMR data are in agreement to the reported ones. In light of these findings, we herein correct the previous stereochemical assignments reported by one of us in the Beilstein J. Org. Chem. 2015, 11, 1922-1932 and the Monatsh. Chem. 2018, 149, 505-517.

Absolute Stereochemistry Determination of Bioactive Marine-Derived Cyclopeptides by Liquid Chromatography Methods: An Update Review (2018-2022).

Cyclopeptides are considered as one of the most important classes of compounds derived from marine sources, due to their structural diversity and a myriad of their biological and pharmacological activities. Since marine-derived cyclopeptides consist of different amino acids, many of which are non-proteinogenic, they possess various stereogenic centers. In this respect, the structure elucidation of new molecular scaffolds obtained from natural sources, including marine-derived cyclopeptides, can become a very challenging task. The determination of the absolute configurations of the amino acid residues is accomplished, in most cases, by performing acidic hydrolysis, followed by analyses by liquid chromatography (LC). In a continuation with the authors' previous publication, and to analyze the current trends, the present review covers recently published works (from January 2018 to November 2022) regarding new cyclopeptides from marine organisms, with a special focus on their biological/pharmacological activities and the absolute stereochemical assignment of the amino acid residues. Ninety-one unreported marine-derived cyclopeptides were identified during this period, most of which displayed anticancer or antimicrobial activities. Marfey's method, which involves LC, was found to be the most frequently used for this purpose.

Synthesis, stereochemical assignment, and enantioselective catalytic activity of late transition metal planar chiral complexes.

Planar chirality is an important form of molecular chirality that can be utilized to induce enantioselectivity when incorporated into transition metal catalysts. However, due to synthetic constraints, the use of late transition metal planar chiral complexes to conduct enantioselective transformations has been limited. Additionally, the published methods surrounding the stereochemical assignment of planar chiral compounds are sometimes conflicting, making proper assignment difficult. This review aims to provide clarity on the methods available to assign planar chirality and provide an overview on the synthesis and use of late transition metal planar chiral complexes as enantioselective catalysts.

Combining the power of DP4+ and ANN-PRA analysis on stereochemical assignments: structural validation of bioactive cyclic peroxide from the marine sponge Plakortis angulospiculatus

Nuclear magnetic resonance (NMR) spectroscopy can provide detailed information about the chemical structure and stereochemistry of a molecule.

Synthesis, Stereochemistry Assignment, and Nmr Structure Elucidation of Icosalide a, and its Analogues: Evaluation of Their Antibacterial, Antituberculosis and Anticancer Activity

Synthesis, Stereochemistry Assignment, and Nmr Structure Elucidation of Icosalide a, and its Analogues: Evaluation of Their Antibacterial, Antituberculosis and Anticancer Activity

Simple, accurate, adjustable-parameter-free prediction of NMR shifts for molecules in solution.

Accurate prediction of NMR shifts is invaluable for interpreting and assigning NMR spectra, especially for complex applications such as determining the identity of unknown substances or resolving stereochemical assignments. Statistical linear regression models have proven effective for accurately correlating density functional theory predictions of chemical shieldings with experimentally-measured shifts, but lack transferability - they must be reparameterised using a reasonably extensive training set at each level of theory and for each choice of NMR solvent. We have previously introduced a novel two-point "shift-and-scale" correction procedure for gas phase shieldings that overcomes these limitations without significant loss of accuracy. In this work, we demonstrate that this approach is equally applicable for predicting solution-phase shifts from computed gas phase shieldings, using acetaldehyde as an experimentally and computationally convenient reference system. We also present all of the required experimental reference data to enable this approach to be used for any target analyte in a range of commonly used NMR solvents (chloroform, dichloromethane, acetonitrile, methanol, acetone, DMSO, D2O, benzene, pyridine).

Highly efficient and scalable total syntheses and stereochemical assignment of potent anti-inflammatory pesimquinolones I and J

A highly efficient and scalable total synthesis of pesimquinolone I (1) was accomplished in 5 steps with 3 chromatographic purifications.

Hyperxylones A and B, two polycyclic polyprenylated acylphloroglucinols with a benzoyl substituted bicyclo[3.2.1]octane core from Hypericum beanii

Two new polycyclic polyprenylated acylphloroglucinols (PPAPs) possessing a rare benzoyl substituted bicyclo[3.2.1]octane core, hyperxylones A (1) and B (2), along with three new dearomatized isoprenylated acylphloroglucinols (DIAPs), hyperxylones C − E (3–5), were isolated from the roots of Hypericum beanii. The structures of 1–5 were determined by high-resolution electrospray ionization mass spectroscopy (HRESIMS) and 1D/2D nuclear magnetic resonance (NMR) spectroscopic analyses, gauge-independent atomic orbital (GIAO) NMR calculations, and electronic circular dichroism (ECD) calculations. Compounds 1 and 2 were biomimetically semi-synthesized starting from 5 and 4, respectively, enabling the correct stereochemical assignment of 5 and 4. Moreover, compounds 1 and 2 showed anti-nonalcoholic steatohepatitis (NASH) activity by inhibiting lipid deposition in L02 cells; compounds 3 and 5 exhibited nitric oxide (NO) inhibitory activity in lipopolysaccharides (LPS)-induced RAW264.7 cells.

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.

GIAO NMR Calculation-Driven Stereochemical Assignment of Marine Macrolide Natural Products: Assessment of the Performance of DP4 and DP4+ Analyses and Assignment of the Relative Configuration of Leptolyngbyalide A–C/Oscillariolide Macrolactone

Abstract The stereochemical assignment of marine macrolide natural products by quantum chemical calculations is often hampered by the generation of an intractable number of conformers in molecular mechanics conformation searches. In this study, we assessed in detail the application of GIAO NMR chemical shift calculation and DP4-type statistical analyses to the stereochemical assignment of two marine macrolide natural products, whose relative configurations had been incorrectly assigned in the originally proposed structures. We also examined how DP4+ probability was affected by cumulative Boltzmann population level of molecular mechanics-derived conformers. Finally, GIAO NMR chemical shift calculation/DP4-type statistical analysis was applied to leptolyngbyalide A–C/oscillariolide macrolactone, whose relative configuration has not been assigned so far.

May the Force (Field) Be with You: On the Importance of Conformational Searches in the Prediction of NMR Chemical Shifts.

NMR data prediction is increasingly important in structure elucidation. The impact of force field selection was assessed, along with geometry and energy cutoffs. Based on the conclusions, we propose a new approach named mix-J-DP4, which provides a remarkable increase in the confidence level of complex stereochemical assignments-100% in our molecular test set-with a very modest increment in computational cost.

Design, Synthesis, and Physicochemical Studies of Configurationally Stable β-Carboline Atropisomers.

Axially chiral atropisomers have energetic barriers to rotation, ΔGrot, that prevent racemization of the respective enantiomers. We used computational modeling to develop a suite of 10 bio-inspired 1-aryl-β-carbolines with varying ΔGrot, from which a strong structure-activity relationship was observed for 2-substituted-1-naphthyl substituents. We then synthesized two of these atropisomers, 1d and 1f, by a four-step racemic synthesis and resolved the enantiomers via chiral chromatography. Racemization studies revealed experimental ΔGrot values of 39.5 and 33.0 kcal/mol for 1d and 1f, respectively, which were consistent with our computational results. These atropisomers exhibited long half-lives, which allowed for their physicochemical characterization and stereochemical assignment via UV-vis spectroscopy, fluorescence spectroscopy, electronic circular dichroism, and vibrational circular dichroism.