Optical Rotation Computation, Total Synthesis, and Stereochemistry Assignment of the Marine Natural Product Pitiamide A

Finding reliable methodology for optical rotation and correct predictions of (s)-methyloxirane and (1R,5R)-β-pinene

Theoretical calculations of optical rotation (OR), although important to predict absolute configurations (ACs) and corroborate experiments, require efficient methodology able to reproduce enantiomer specificity and real OR values. Also, troublesome molecules are recurring in the literature, such as (S)-methyloxirane and (1R,5R)-β-pinene. This study evaluates DFT functionals B3LYP, CAM-B3LYP, ωB97X-D, M06-2X, and PBE0 considering basis sets aug-cc-pVDZ, aug-cc-pVTZ, 6-311++G(2d,p), and 6-311++G(3df,2p) in OR prediction of 42 rigid organic molecules assessing cases with wrong enantiomeric determination comparing to available experimental data at wavelengths 355, 589, and 633 nm. Functionals CAM-B3LYP and ωB97X-D with aug-cc-pVTZ are indicated here to reproduce experimental values more accurately considering fewer number of wrong AC predictions, normalized RMSD values below 0.70, and a good approximation to experimental values in hierarchical cluster analysis. Methyloxirane AC was reproduced in CAM-B3LYP and PBE0, with [ α ] 355 = 6 . 94 $$ {\left[\alpha \right]}_{355}=6.94 $$ for CAM-B3LYP/aug-cc-pVTZ close to experimental value [ α ] 355 = 7 . 49 ± 0 . 30 $$ {\left[\alpha \right]}_{355}=7.49\pm 0.30 $$ . Good results were found for AC of β-pinene in M06-2X, CAM-B3LYP, and ωB97X-D while the latter in 6-311++G(3df,2p) obtained OR values of [ α ] 589 = 3 . 44 $$ {\left[\alpha \right]}_{589}=3.44 $$ and [ α ] 689 = 4 . 20 $$ {\left[\alpha \right]}_{689}=4.20 $$ close to experimental values [ α ] 589 = 2 . 8 $$ {\left[\alpha \right]}_{589}=2.8 $$ and [ α ] 689 = 4 . 66 ± 0 . 60 $$ {\left[\alpha \right]}_{689}=4.66\pm 0.60 $$ . The two molecules aforementioned are, for the first time, reported to give valid theoretical OR values in such simple methodologies. OR calculations were all performed after geometry optimization at the same level of theory, and analysis of different functional combinations for each step in β-pinene showed it can interfere with AC prediction even in rigid molecules.

Automated Quantum Chemistry-Based Calculation of Optical Rotation for Large Flexible Molecules

The calculation of optical rotation (OR, [α]_D) for nonrigid molecules was limited to small systems due to the challenging problem of generating reliable conformer ensembles, calculating accurate Boltzmann populations and the extreme sensitivity of the OR to the molecules' three-dimensional structure. Herein, we describe and release the crenso workflow for the automated computation of conformer ensembles in solution and corresponding [α]_D values for flexible molecules. A comprehensive set of 28 organic drug molecules (28-144 atoms) with experimentally determined values is used in our assessment. In all cases, the correct OR sign is obtained with an overall mean relative deviation of 72% (mean absolute deviation of 82 °[dm(g/cm³)]^-1 for experimental values in the range -160 to 287 °[dm(g/cm³)]^-1). We show that routine [α]_D computations for very flexible, biologically active molecules are both feasible and reproducible in about a day of computation time on a standard workstation computer. Furthermore, we observed that the effect of energetically higher-lying structures in the ensemble on the OR is often averaged out and that in 23 out of 28 cases, the correct OR sign is obtained by just considering only the lowest free energy conformer. In four example cases, we show that the approach can also describe the OR of pairs of flexible diastereomers properly. In summary, even very sensitive, multifactorial physicochemical properties appear reliably predictable with minimal user input from efficiently automated quantum chemical methods.

Bioactivity Potential of Marine Natural Products from Scleractinia-Associated Microbes and In Silico Anti-SARS-COV-2 Evaluation

Marine organisms and their associated microbes are rich in diverse chemical leads. With the development of marine biotechnology, a considerable number of research activities are focused on marine bacteria and fungi-derived bioactive compounds. Marine bacteria and fungi are ranked on the top of the hierarchy of all organisms, as they are responsible for producing a wide range of bioactive secondary metabolites with possible pharmaceutical applications. Thus, they have the potential to provide future drugs against challenging diseases, such as cancer, a range of viral diseases, malaria, and inflammation. This review aims at describing the literature on secondary metabolites that have been obtained from Scleractinian-associated organisms including bacteria, fungi, and zooxanthellae, with full coverage of the period from 1982 to 2020, as well as illustrating their biological activities and structure activity relationship (SAR). Moreover, all these compounds were filtered based on ADME analysis to determine their physicochemical properties, and 15 compounds were selected. The selected compounds were virtually investigated for potential inhibition for SARS-CoV-2 targets using molecular docking studies. Promising potential results against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and methyltransferase (nsp16) are presented.

Structural Diversity, Biological Properties and Applications of Natural Products from Cyanobacteria. A Review

Nowadays, various drugs on the market are becoming more and more resistant to numerous diseases, thus declining their efficacy for treatment purposes in human beings. Antibiotic resistance is one among the top listed threat around the world which eventually urged the discovery of new potent drugs followed by an increase in the number of deaths caused by cancer due to chemotherapy resistance as well. Accordingly, marine cyanobacteria, being the oldest prokaryotic microorganisms belonging to a monophyletic group, have proven themselves as being able to generate pharmaceutically important natural products. They have long been known to produce distinct and structurally complex secondary metabolites including peptides, polyketides, alkaloids, lipids, and terpenes with potent biological properties and applications. As such, this review will focus on recently published novel compounds isolated from marine cyanobacteria along with their potential bioactivities such as antibacterial, antifungal, anticancer, anti-tuberculosis, immunosuppressive and anti-inflammatory capacities. Moreover, various structural classes, as well as their technological uses will also be discussed.

Applied circular dichroism: a facile spectroscopic tool for configurational assignment and determination of enantiopurity

In order to determine if electronic circular dichroism (ECD) is a good tool for the qualitative evaluation of absolute configuration and enantiopurity in the absence of chiral high performance liquid chromatography (HPLC), ECD studies were performed on several prescriptions and over-the-counter drugs. Cotton effects (CE) were observed for both S and R isomers between 200 and 300 nm. For the drugs examined in this study, the S isomers showed a negative CE, while the R isomers displayed a positive CE. The ECD spectra of both enantiomers were nearly mirror images, with the amplitude proportional to the enantiopurity. Plotting the differential extinction coefficient (Δε) versus enantiopurity at the wavelength of maximum amplitude yielded linear standard curves with coefficients of determination (R (2)) greater than 97% for both isomers in all cases. As expected, Equate, Advil, and Motrin, each containing a racemic mixture of ibuprofen, yielded no chiroptical signal. ECD spectra of Suphedrine and Sudafed revealed that each of them is rich in 1S,2S-pseudoephedrine, while the analysis of Equate vapor inhaler is rich in R-methamphetamine.

Indole-based alkaloids from deep-sea bacterium Shewanella piezotolerans with antitumor activities

Chromatographic separation of a crude extract obtained from a fermentation broth of a chemically unknown bacterium Shewanella piezotolerans WP3 collected in deep-sea yielded three new indole alkaloids namely shewanellines A (1a), B (1b) and C (2), together with 12 known indole alkaloids. The structures were unambiguously elucidated on the basis of 1D and 2D NMR ((1)H, (13)C, COSY, HMBC, HSQC and NOESY) in association with MS and CD data. Compounds 1-4, 7, 9 and 11-14 were selected for the evaluation of their cytotoxic activities against human tumor cell lines HL-60 and BEL-7402, whereas compounds 2, 4 and 9 exhibited significant inhibition toward HL-60.

A tetraene aldehyde as the major sex pheromone component of the promethea moth (Callosamia promethea (Drury))

The promethea moth Callosamia promethea is one of three species of silkmoths from the genus Callosamia that occur in North America. Cross attraction of males to heterospecific calling females has been observed in the field, and hybrid progeny have been produced by pairing heterospecifics in captivity. These observations suggest that all three species share or have considerable overlap in the sex attractant pheromones produced by females, so that other prezygotic isolating mechanisms, such as diel differences in reproductive activity, limit hybridization in the field. Coupled gas chromatography-electroantennogram detection and gas chromatography- mass-spectrometry analyses of extracts of volatiles collected from female promethea moths supported the identification of (4E,6E,11Z,13Z)-hexadeca-4,6,11,13-tetraenal [(4E,6E,11Z,13Z)-16:Ald] as the compound in extracts that elicited the largest responses from antennae of males. The identification was confirmed by non-selective synthesis of several isomers as analytical standards, and stereoselective synthesis of (4E,6E,11Z,13Z)-16:Ald for testing in field trials. Male moths were strongly attracted to synthetic (4E,6E,11Z,13Z)-16:Ald, suggesting that this compound is the major and possibly the only component of the sex pheromone of these large saturniid moths. Based on the cross-attraction of heterospecifics, it is likely that this is also a major pheromone component of the other two North American Callosamia species as well.

Plakortolide stereochemistry revisited: the checkered history of plakortolides e and I

The relative configuration of the plakortolide metabolite (4) isolated from a Madagascan Plakortis sp. and named (+)-plakortolide I is revised following reassignment of the ¹³C signals for C-7 and C-16, thereby establishing that the metabolite isolated was likely (+)-plakortolide E (3). We propose that the name "plakortolide I" should be retained for the plakortolide metabolite 5 first isolated by the Faulkner group; its enantiomer 4 can then be named ent-plakortolide I in line with the description of Barnych and Vatèle. The spectroscopic data for MPA esters prepared from synthetic samples of seco derivatives of plakortolide E (3) and ent-plakortolide I (4) were compared with those of MPA esters of seco derivatives from naturally isolated plakortolides L (1) and K (2) and of seco-plakortolide E (6a). Likewise, the spectroscopic data for MTPA esters derived from 3 and 4 were compared with data for the MTPA esters derived from 5. These various comparisons established that the sign of the specific rotation associated with the natural isolates is an unreliable indicator of absolute configuration and verify that the absolute configurations of plakortolides L (1), K (2), E (3), and I (5) are (3S, 4S, 6S), (3R, 4R, 6S), (3R, 4R, 6R), and (3S, 4S, 6R), respectively.

Identification of the sex pheromone of a protected species, the Spanish moon moth Graellsia isabellae

Sex attractant pheromones are highly sensitive and selective tools for detecting and monitoring populations of insects, yet there has been only one reported case of pheromones being used to monitor protected species. Here, we report the identification and synthesis of the sex pheromone of a protected European moth species, Graellsia isabellae (Lepidoptera: Saturniidae), as the single component, (4E,6E,11Z)-hexadecatrienal. In preliminary field trials, lures loaded with this compound attracted male moths from populations of this species at a number of widely separated field sites in France, Switzerland, and Spain, clearly demonstrating the utility of pheromones in sampling potentially endangered insect species.

Optical signatures of molecular dissymmetry: combining theory with experiments to address stereochemical puzzles

Modern chemistry emerged from the quest to describe the three-dimensional structure of molecules: van't Hoff's tetravalent carbon placed symmetry and dissymmetry at the heart of chemistry. In this Account, we explore how modern theory, synthesis, and spectroscopy can be used in concert to elucidate the symmetry and dissymmetry of molecules and their assemblies. Chiroptical spectroscopy, including optical rotatory dispersion (ORD), electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA), measures the response of dissymmetric structures to electromagnetic radiation. This response can in turn reveal the arrangement of atoms in space, but deciphering the molecular information encoded in chiroptical spectra requires an effective theoretical approach. Although important correlations between ECD and molecular stereochemistry have existed for some time, a battery of accurate new theoretical methods that link a much wider range of chiroptical spectroscopies to structure have emerged over the past decade. The promise of this field is considerable: theory and spectroscopy can assist in assigning the relative and absolute configurations of complex products, revealing the structure of noncovalent aggregates, defining metrics for molecular diversity based on polarization response, and designing chirally imprinted nanomaterials. The physical organic chemistry of chirality is fascinating in its own right: defining atomic and group contributions to optical rotation (OR) is now possible. Although the common expectation is that chiroptical response is determined solely by a chiral solute's electronic structure in a given environment, chiral imprinting effects on the surrounding medium and molecular assembly can, in fact, dominate the chiroptical signatures. The theoretical interpretation of chiroptical markers is challenging because the optical properties are subtle, resulting from the strong electric dipole and the weaker electric quadrupole and magnetic dipole perturbations by the electromagnetic field. Moreover, OR arises from a combination of nearly canceling contributions to the electronic response. Indeed, the challenge posed by the chiroptical properties delayed the advent of even qualitatively accurate descriptions for some chiroptical signatures until the past decade when, for example, prediction of the observed sign of experimental OR became accessible to theory. The computation of chiroptical signatures, in close coordination with synthesis and spectroscopy, provides a powerful framework to diagnose and interpret the dissymmetry of chemical structures and molecular assemblies. Chiroptical theory now produces new schemes to elucidate structure, to describe the specific molecular sources of chiroptical signatures, and to assist in our understanding of how dissymmetry is templated and propagated in the condensed phase.

Absolute Configuration of Conformationally Flexiblecis-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.

Transition-metal-mediated cascade reactions: the water-accelerated carboalumination-Claisen rearrangement-carbonyl addition reaction

[Chemical reaction: See text] A three-step cascade reaction involving a water-accelerated catalytic carboalumination, a Claisen rearrangement, and a nucleophilic carbonyl addition converts terminal alkynes and allyl vinyl ethers into allylic alcohols containing up to three contiguous asymmetric carbon centers. Stoichiometric quantities of water as an additive increase the rate of the [3,3] sigmatropic rearrangement as well as the diastereoselectivity of the carbonyl addition process. Reaction products contain 1,6-diene functionalities that are readily cyclized to substituted cyclopentenes. An extension of this methodology to a sequence involving a [1,3] sigmatropic shift was feasible with a cyclopropylmethyl vinyl ether substrate.

Synthesis of the 3-Aza-[7]-paracyclophane Core of Haouamine A and B

[reaction: see text] The synthesis of the highly strained 3-aza-[7]-paracyclophane core of haouamines A and B is based on a macrocyclization-aromatization protocol, allowing for a stepwise increase in ring strain and establishing the oxygenation pattern of the natural products.

Stereochemistry of oxachlorocarbene S(N)i reactions

[reaction: see text] 3-Nortricyclyloxychlorocarbene and trans-4-methylcyclohexyloxychlorocarbene both fragment in hydrocarbon solvents with extensive loss of stereochemical integrity to the corresponding chlorides via competitive and nearly isoenergetic S(N)i-like transition states.

Synthesis of the C1–C16 fragment of ionomycin using a neutral (η3-allyl)iron complex

Key steps in the synthesis of the C1-C16 polyketide fragment of ionomycin were the nucleophilic addition of an organocuprate to a neutral (eta3-allyl)iron complex and the construction of a beta-diketone moiety by the Rh-catalysed rearrangement of an alpha-diazo-beta-hydroxyketone.

Determination of the Absolute Configuration of Flexible Molecules byab InitioORD Calculations: A Case Study with Cytoxazones and Isocytoxazones

Ab initio calculations of the optical rotatory power of the natural cytokine modulator cytoxazone 1 and its trans-diastereomer 2, as well as the structural isomers cis-3 and trans-4 isocytoxazones, have been performed at four different wavelengths (589, 546, 435, and 405 nm) by Density Functional Theory. The calculation of ORD curves provides a reliable method for the assignment of absolute configuration of these conformationally flexible molecules. The absolute configurations of isocytoxazones has been established as (+)-(4R,5S)-cis-3 and (+)-(4S,5S)-trans-4.

Determination of absolute configuration using density functional theory calculation of optical rotation: chiral alkanes

The recently developed Gauge-Invariant (Including) Atomic Orbital (GIAO) based Time-Dependent Density Functional Theory (TDDFT) methodology for the calculation of transparent spectral region optical rotations of chiral molecules provides a new approach to the determination of absolute configurations. Here, we discuss the application of the TDDFT/GIAO methodology to chiral alkanes. We report B3LYP/aug-cc-pVDZ calculations of the specific rotations of the 22 chiral alkanes, 2-23, of well-established Absolute Configuration. The average absolute deviation of calculated and experimental [alpha](D) values for molecules 2-22 is 24.8. In two of the molecules 2-23, trans-pinane, 10, and endo-isocamphane, 13, the sign of [alpha](D) is incorrectly predicted. Our results demonstrate that absolute configurations of alkanes can be reliably assigned by using B3LYP/aug-cc-pVDZ TDDFT/GIAO calculations if, but only if, [alpha](D) is significantly greater than 25. In the case of (-)-anti-trans-anti-trans-anti-trans-perhydrotriphenylene, 1, [alpha](D) is -93 and TDDFT/GIAO calculations reliably lead to the absolute configuration R(-).

Assignment of the absolute configuration of [n]-ladderanes by TD-DFT optical rotation calculations

In this study, we report theoretical specific rotation values for a series of cis-/trans-alkylated-[5]-ladderanes and cis-/trans-methylated-[n]-ladderanes. Using time-dependent density functional response theory optical rotation calculations, we can assign (+) and (-) optical rotation signs to trans-(S)-alkyl-[5]-ladderane and trans-(R)-alkyl-[5]-ladderane configurations, respectively. In order to qualitatively validate our absolute configuration predictions, we computed optical rotation values at three different levels of theory--B3LYP, RI-BP86, and Hartree-Fock--using the aug-cc-pVDZ basis set. We observe a novel rung-parity-controlled oscillatory optical rotatory phenomenon in our computations, which, to the best of our knowledge, has never been reported or observed before. Furthermore, this preliminary analysis of optical rotation properties in this class of compounds should facilitate the correct absolute stereochemical assignment of natural and synthetic ladderanes, such as the trans-isomer of pentacyclic C(20)-fatty acid methyl ester (pentacycloanammoxic methyl ester), without the need for derivatization, in particular for cases where NMR or X-ray crystal structures are not readily available.

Total synthesis and structure validation of (+)-bistramide C

The convergent total synthesis of the marine natural product (+)-bistramide C confirms the a priori assignments of its relative and absolute configurations, which were originally based on the combined application of [alpha]D analysis, NMR, and synthesis.