DFT-supported structure determination of gymunomitr-3(15)-en-4b,9b-diol

Matsumoto, Manami; Miura, Satomi; Tonouchi, Akio; Hashimoto, Minoru

doi:10.1016/j.tet.2020.131301

Cited by 3 publications

(4 citation statements)

References 18 publications

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“…With the relative structures of 1 – 3 established, we investigated their absolute configurations by comparing their experimental electronic circular dichroism (ECD) spectra with those generated from DFT calculations. We chose CAM-B3LYP/def2-TZVP under vacuum conditions for geometry optimizations, energy calculations, and spectrum reproductions based on the successful outcomes in our previous studies …”

Section: Resultsmentioning

confidence: 99%

Isolation of Paraphaeoketones: A Plausible Biosynthetic Explanation for Paraphaeolactones via a Benzilic Acid Rearrangement Rather than a Favorskii Rearrangement

Oinuma,

Kanehara,

Maeda

et al. 2024

J. Nat. Prod.

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Paraphaeoketones A−C (1−3) were isolated from the culture broth of Paraphaeosphaeria sp. KT4192. Their structures and relative configurations were determined using spectroscopic analysis and verified through density functional theory (DFT)-based chemical shift calculations. The absolute configurations of these compounds were determined by comparing the experimental electronic circular dichroism (ECD) spectra with those based on DFT calculations. We also propose a plausible biosynthetic route to 1−3. While our prior studies on the isolation and structural elucidation of paraphaeolactones (e.g., 4) led us to suggest a Favorskii rearrangement for their biosynthesis, the isolation of 2 prompted the proposal of an alternative biosynthesis for 4, featuring a benzilic acid rearrangement of 2. Moreover, an in vitro conversion of 2 into 4 was achieved successfully, suggesting that a biosynthetic pathway for paraphaeolactones involving a benzilic acid rearrangement is more plausible than the previously presumed Favorskii rearrangement pathway. Arguments based on DFT calculations for these pathways are also described.

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Section: Resultsmentioning

confidence: 99%

Isolation of Paraphaeoketones: A Plausible Biosynthetic Explanation for Paraphaeolactones via a Benzilic Acid Rearrangement Rather than a Favorskii Rearrangement

Oinuma,

Kanehara,

Maeda

et al. 2024

J. Nat. Prod.

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“…In several recent studies, structures have been determined by comparing calculated NMR and ECD spectra with experimental ones. − However, this method is unreliable for flexible molecules. Therefore, we decided to model all reaction routes to identify the main expected product.…”

Section: Resultsmentioning

confidence: 99%

Stereochemistries and Biological Properties of Oligomycin A Diels–Alder Adducts

et al. 2021

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Oligomycin A is a potent antibiotic and antitumor agent. However, its applications are restricted by its high toxicity and low bioavailability. In this study, we obtained Oligomycin A Diels− Alder adducts with benzoquinone and N-benzylmaleimide and determined their absolute configurations by combining 1 H and ROESY NMR data with molecular mechanics conformational analysis and quantum chemical reaction modeling. The latter showed that adduct stereochemistry is controlled by hydrogen bonding of the Oligomycin A side-chain isopropanol moiety with the carbonyl group of the dienophile. Biological studies showed that the Diels−Alder modification of the Oligomycin A diene system resulted in a complex antiproliferative potential pattern. The synthesized adducts were determined to be more active against the triple-negative (ERα, PR, and HER2 negative) breast cancer cell line MDA-MB-231 and lung carcinoma cell line A-549 compared to Oligomycin A. Meanwhile, Oligomycin A was more potent against myeloid leukemia cell line K-562 and breast carcinoma cell line MCF-7 than its derivatives. Thus, modification of the diene moiety of Oligomycin A is a promising strategy for developing novel antitumor agents based on its scaffold.

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“…However, information solely on chemical shifts in experimental and calculated spectra is often insufficient. But the combination of DFT calculations, spectral experiments, and additional experiments on circular dichroism provides a reliable possibility of establishing the configuration of stereocenters in complex and flexible natural compounds, such as for cyclohelmintols, seiricardine B, and gymnomitr-3(15)-en-4 b ,9 b -diol . As an alternative, a two-criterion method, a combination of nuclear spin–spin interaction and 13 C chemical shifts, was considered as applied to structures of halogenated terpenoids …”

Section: Introductionmentioning

confidence: 99%

“…But the combination of DFT calculations, spectral experiments, and additional experiments on circular dichroism provides a reliable possibility of establishing the configuration of stereocenters in complex and flexible natural compounds, such as for cyclohelmintols, 10 seiricardine B, 11 and gymnomitr-3(15)-en-4b,9b-diol. 12 As an alternative, a two-criterion method, a combination of nuclear spin−spin interaction and 13 C chemical shifts, was considered as applied to structures of halogenated terpenoids. 13 The following protocol for calculating 13 C NMR chemical shifts for natural products with several degrees of conformational freedom was found to be effective (rms <4 ppm).…”

Section: ■ Introductionmentioning

confidence: 99%

Pseudocyclic Form of 4-Hydroxypyrrolidine-2-carboxanilide Podands with Trioxyethylene Chain: Modeling, Conformational Search, and NMR Analysis

et al. 2021

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The 4-hydroxypyrrolidine-2-carboxanilide podand salt demonstrates catalytic activity in asymmetric Biginelli reaction. The systematic search for prevalent conformational state of the cation was carried out by computer simulations in combination with one-and two-dimensional NMR experiments. For that purpose, we proposed a novel algorithm for the generation and selection of conformers based on molecular dynamics and clustering in the space of principal components. The search had found an important trend of the podand to form a pseudocyclic structure with a horseshoe-shaped conformation of the oligooxyethylene fragment. This conformation is stabilized by different types of intramolecular hydrogen bonds between the acidic and basic centers of the two 4-hydroxypyrrolidine-2-carboxanilide residuals (branches). The proposed approach had made it possible to identify the major structural factors, providing a correlation between the calculated and experimental chemical shifts of hydrogen atoms in the 1 H NMR spectra of the protonated podand.

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DFT-supported structure determination of gymunomitr-3(15)-en-4b,9b-diol

Cited by 3 publications

References 18 publications

Isolation of Paraphaeoketones: A Plausible Biosynthetic Explanation for Paraphaeolactones via a Benzilic Acid Rearrangement Rather than a Favorskii Rearrangement

Isolation of Paraphaeoketones: A Plausible Biosynthetic Explanation for Paraphaeolactones via a Benzilic Acid Rearrangement Rather than a Favorskii Rearrangement

Stereochemistries and Biological Properties of Oligomycin A Diels–Alder Adducts

Pseudocyclic Form of 4-Hydroxypyrrolidine-2-carboxanilide Podands with Trioxyethylene Chain: Modeling, Conformational Search, and NMR Analysis

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