Synthesis and Structural Revision of Phomopsin B, a Novel Polyketide Carrying a 10-Membered Cyclic-Ether Ring

Izuchi, Yuko; Koshino, Hiroyuki; Hongo, Yayoi; Kanomata, Nobuhiro; Takahashi, Shigetoshi

doi:10.1021/ol2011117

Cited by 18 publications

(13 citation statements)

References 25 publications

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“…This study represents the first total synthesis of compounds 10c , 10d , 10f , 10g , 10h , and 10i . While we generally observed good agreement between our spectroscopic data and the data presented in the isolation reports, we found significant deviations in the 1 H and 13 C NMR data for compound 10f (see SI for a comparison table).…”

Section: Resultssupporting

confidence: 92%

Rhodium-Phosphoramidite Catalyzed Alkene Hydroacylation: Mechanism and Octaketide Natural Product Synthesis

2012

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We describe a method that allows salicylaldehyde derivatives to be coupled with a wide range of unactivated alkenes at catalyst loadings as low as 2 mol %. A chiral phosphoramidite ligand and the precise stoichiometry of heterogeneous base are key for high catalytic activity and linear regioselectivity. This protocol was applied in the atom- and step-economical synthesis of eight biologically active octaketide natural products, including anticancer drug candidate cytosporone B. Mechanistic studies provide insight on parameters affecting decarbonylation, a side reaction that limits the turnover number for catalytic hydroacylation. Deuterium labeling studies show that branched hydride insertion is fully reversible, whereas linear hydride insertion is largely irreversible and turnover-limiting. We propose that ligand (R(a),R,R)-SIPHOS-PE effectively suppresses decarbonylation, and helps favor a turnover-limiting insertion, by lowering the barrier for reductive elimination in the linear-selective pathway. Together, these factors enable high reactivity and regioselectivity.

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Section: Resultssupporting

confidence: 92%

Rhodium-Phosphoramidite Catalyzed Alkene Hydroacylation: Mechanism and Octaketide Natural Product Synthesis

2012

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“…The authors suggested that the structure of phomopsin A was likely to require revision to that of dothioreline B 310 but as the 13 C NMR data of the two compounds were not identical, it might indicate that the 13 C NMR assignments for dothiorelone B also need reinvestigation. 311 Seragakinone A was originally isolated from an unidentied red alga-associated fungus. 312 The absolute conguration of the subsequently corrected structure 313 has been conrmed by synthesis of the enantiomer, (À)-seragakinone A.…”

Section: Synthetic Aspectsmentioning

confidence: 99%

Marine natural products

et al. 2013

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This review covers the literature published in 2011 for marine natural products, with 870 citations (558 for the period January to December 2011) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1152 for 2011), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

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“…However, sometimes, we could not obtain the structural fragments of a molecule and could only rely on the NMR and molecular formula for structural elucidation. To evaluate the performance of CMGNet with NMR and the molecular formula as conditions, we collected nine 13 C NMR spectra, whose originally determined structures were revised in later publications. − In this task, we examined whether the model generated the correct molecules or preferentially generated the correct molecules by comparing the ranks of original structures and revised structures. Table shows four molecules that were not included in the training set.…”

Section: Resultsmentioning

confidence: 99%

Conditional Molecular Generation Net Enables Automated Structure Elucidation Based on ¹³C NMR Spectra and Prior Knowledge

Yao¹,

Yang

Song³

et al. 2023

Anal. Chem.

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Structure elucidation of unknown compounds based on nuclear magnetic resonance (NMR) remains a challenging problem in both synthetic organic and natural product chemistry. Library matching has been an efficient method to assist structure elucidation. However, it is limited by the coverage of libraries. In addition, prior knowledge such as molecular fragments is neglected. To solve the problem, we propose a conditional molecular generation net (CMGNet) to allow input of multiple sources of information. CMGNet not only uses 13C NMR spectrum data as input but molecular formulas and fragments of molecules are also employed as input conditions. Our model applies large-scale pretraining for molecular understanding and fine-tuning on two NMR spectral data sets of different granularity levels to accommodate structure elucidation tasks. CMGNet generates structures based on 13C NMR data, molecular formula, and fragment information, with a recovery rate of 94.17% in the top 10 recommendations. In addition, the generative model performed well in the generation of various classes of compounds and in the structural revision task. CMGNet has a deep understanding of molecular connectivities from 13C NMR, molecular formula, and fragments, paving the way for a new paradigm of deep learning-assisted inverse problem-solving.

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Synthesis and Structural Revision of Phomopsin B, a Novel Polyketide Carrying a 10-Membered Cyclic-Ether Ring

Cited by 18 publications

References 25 publications

Rhodium-Phosphoramidite Catalyzed Alkene Hydroacylation: Mechanism and Octaketide Natural Product Synthesis

Rhodium-Phosphoramidite Catalyzed Alkene Hydroacylation: Mechanism and Octaketide Natural Product Synthesis

Marine natural products

Conditional Molecular Generation Net Enables Automated Structure Elucidation Based on ¹³C NMR Spectra and Prior Knowledge

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Synthesis and Structural Revision of Phomopsin B, a Novel Polyketide Carrying a 10-Membered Cyclic-Ether Ring

Cited by 18 publications

References 25 publications

Rhodium-Phosphoramidite Catalyzed Alkene Hydroacylation: Mechanism and Octaketide Natural Product Synthesis

Rhodium-Phosphoramidite Catalyzed Alkene Hydroacylation: Mechanism and Octaketide Natural Product Synthesis

Marine natural products

Conditional Molecular Generation Net Enables Automated Structure Elucidation Based on 13C NMR Spectra and Prior Knowledge

Contact Info

Product

Resources

About

Conditional Molecular Generation Net Enables Automated Structure Elucidation Based on ¹³C NMR Spectra and Prior Knowledge