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Zhou Y, Limbu I, Garson MJ, Krenske EH. Conformational Sampling in Computational Studies of Natural Products: Why Is It Important? JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 39315508 DOI: 10.1021/acs.jnatprod.4c00852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.
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Affiliation(s)
- Yuchen Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Ingso Limbu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Mary J Garson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
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2
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Priessner M, Lewis RJ, Johansson MJ, Goodman JM, Janet JP, Tomberg A. HSQC Spectra Simulation and Matching for Molecular Identification. J Chem Inf Model 2024; 64:3180-3191. [PMID: 38533705 DOI: 10.1021/acs.jcim.3c01735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
In the pursuit of improved compound identification and database search tasks, this study explores heteronuclear single quantum coherence (HSQC) spectra simulation and matching methodologies. HSQC spectra serve as unique molecular fingerprints, enabling a valuable balance of data collection time and information richness. We conducted a comprehensive evaluation of the following four HSQC simulation techniques: ACD/Labs (ACD), MestReNova (MNova), Gaussian NMR calculations (DFT), and a graph-based neural network (ML). For the latter two techniques, we developed a reconstruction logic to combine proton and carbon 1D spectra into HSQC spectra. The methodology involved the implementation of three peak-matching strategies (minimum-sum, Euclidean-distance, and Hungarian distance) combined with three padding strategies (zero-padding, peak-truncated, and nearest-neighbor double assignment). We found that coupling these strategies with a robust simulation technique facilitates the accurate identification of correct molecules from similar analogues (regio- and stereoisomers) and allows for fast and accurate large database searches. Furthermore, we demonstrated the efficacy of the best-performing methodology by rectifying the structures of a set of previously misidentified molecules. This research indicates that effective HSQC spectral simulation and matching methodologies significantly facilitate molecular structure elucidation. Furthermore, we offer a Google Colab notebook for researchers to use our methods on their own data (https://github.com/AstraZeneca/hsqc_structure_elucidation.git).
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Affiliation(s)
- Martin Priessner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Richard J Lewis
- Department of Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Magnus J Johansson
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jonathan M Goodman
- Centre for Molecular Informatics, The Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jon Paul Janet
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Anna Tomberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
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3
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Xie F, Xia DD, Duan HJ, Sun Y, Zi ZF, Wan DY, Zhou H, Ding ZT. Two Decarestrictine Analogs from the Soil-Derived Fungus Penicillium sp. YUD18003 Associated with Gastrodia elata. Chem Biodivers 2023; 20:e202300566. [PMID: 37365441 DOI: 10.1002/cbdv.202300566] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 06/28/2023]
Abstract
Two new decarestrictine analogs decarestrictine P and penicitone, together with eight known homologous compounds were isolated from the soil fungus from the rhizosphere of Penicillium sp. YUD18003 related to Gastrodia elata. Their different structures include a decanolides decartestridine P and a long-chain polyhydroxyketone penicitone. The structures of new compounds were determined by nuclear magnetic resonance (NMR) spectroscopic analysis and high resolution electrospray ionization mass spectrometry (HR-ESI-MS), while their absolute configurations were determined by spectroscopic methods, DP4+ probability analysis, modified Snatzke's method and electron circular dichroism (ECD) calculations. All compounds were evaluated for antimicrobial activities.
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Affiliation(s)
- Fei Xie
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650500, China
| | - Dan-Dan Xia
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Hao-Jie Duan
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Yue Sun
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Zhi-Feng Zi
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Dai-Yu Wan
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Hao Zhou
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
| | - Zhong-Tao Ding
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Yunnan Characteristic Plant Extraction Laboratory, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
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4
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Hoyt EM, Smith LO, Crittenden DL. Simple, accurate, adjustable-parameter-free prediction of NMR shifts for molecules in solution. Phys Chem Chem Phys 2023; 25:9952-9957. [PMID: 36951928 DOI: 10.1039/d3cp00721a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
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).
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Affiliation(s)
- Emlyn M Hoyt
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Lachlan O Smith
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand.
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5
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Wang CY, Gan D, Li CZ, Zhang SQ, Li BX, Zhu L, Liu JQ, Liu H, Tuo GT, Zhang FM, Cai L. A New Highly Oxygenated Polyketide Derivative from Trichoderma sp. and Its Antifungal Activity. Chem Biodivers 2022; 19:e202200671. [PMID: 36373236 DOI: 10.1002/cbdv.202200671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
A new highly oxygenated polyketide derivative, trichodersine (1), together with fourteen known compounds (2-15) were isolated from Trichoderma sp. MWTGP-04. The structure of trichodersine (1) was established based on comprehensive spectroscopic data analysis, and biogenesis argument. The results of double culture experiments indicated that the strain exhibited potential antifungal activity. The antifungal activities of all isolated compounds were evaluated, among them compound 1 exhibited remarkable antifungal activities against Fusarium solani, Plectosphaerella cucumerina, Alternaria panax, and Aspergillus niger, with minimum inhibitory concentrations (MICs) of 4, 4, 16, and 32 μg/mL, respectively. In addition, the antifungal experiments of polyketide derivatives (1-3) disclosed that their degree of oxidation was a key factor affecting the antifungal activity.
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Affiliation(s)
- Cheng-Yao Wang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Dong Gan
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Chen-Zhe Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Sheng-Qi Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Bin-Xian Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Li Zhu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Jia-Qi Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Han Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Gui-Tao Tuo
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Feng-Mei Zhang
- R&D Center of China Tobacco Yunnan Industry Co., Ltd., Kunming, 650231, P. R., China
| | - Le Cai
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
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6
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Yesiltepe Y, Govind N, Metz TO, Renslow RS. An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts. J Cheminform 2022; 14:64. [PMID: 36138446 PMCID: PMC9499888 DOI: 10.1186/s13321-022-00587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/06/2022] [Indexed: 11/24/2022] Open
Abstract
The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13C and 1H NMR spectra with respect to experimentally measured values. This leads us to the question-what accuracy is required in predicted 13C and 1H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1H and 13C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.
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Affiliation(s)
- Yasemin Yesiltepe
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Niranjan Govind
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Ryan S Renslow
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA.
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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7
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Li J, Tan YF, Liu S, Wu XQ, Wang J, Xu KP, Tan GS, Zou ZX, Wang WX. Reassignment of the structures of pestalopyrones A-D. PHYTOCHEMISTRY 2022; 200:113205. [PMID: 35436477 DOI: 10.1016/j.phytochem.2022.113205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/10/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Pestalopyrones A-D are four unusual tricyclic pyrone derivatives with flexible chiral structures, isolated from the endophytic fungus Pestalotiopsis neglecta S3. The full elucidation of their structures was a challenging task, and remained unsolved in the original article. Herein, the relative configurations of pestalopyrones A and pestalopyrones B were unambiguously assigned by detailed analyses on spectroscopic data and GIAO 13C NMR calculation method with sorted training sets (STS). The planar structures of pestalopyrones C and pestalopyrones D were revised by reinterpretation of their reported spectroscopic data, and then their relative configurations were deduced by STS GIAO 13C NMR calculation and NOE analysis. The absolute configurations of all the mentioned compounds were determined by the comparison of their experimental and calculated ECD curves.
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Affiliation(s)
- Jing Li
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Yu-Fen Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Xiao-Qian Wu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Kang-Ping Xu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Gui-Shan Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Zhen-Xing Zou
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China.
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8
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Elyashberg M, Novitskiy IM, Bates RW, Kutateladze AG, Williams CM. Reassignment of Improbable Natural Products Identified through Chemical Principle Screening. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development Inc. (ACD/Labs) Toronto ON, M5C 1B5 Canada
| | - Ivan M. Novitskiy
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Roderick W. Bates
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Andrei G. Kutateladze
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Queensland Australia
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9
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Novitskiy IM, Kutateladze AG. Peculiar Reaction Products and Mechanisms Revisited with Machine Learning-Augmented Computational NMR. J Org Chem 2022; 87:8589-8598. [PMID: 35723522 DOI: 10.1021/acs.joc.2c00749] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DU8ML, a fast and accurate machine learning-augmented density functional theory (DFT) method for computing nuclear magnetic resonance (NMR) spectra, proved effective for high-throughput revision of misassigned natural products. In this paper, we disclose another important aspect of its application: correction of unusual reaction mechanisms originally proposed because of incorrect product structures.
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Affiliation(s)
- Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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10
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Novitskiy IM, Kutateladze AG. DU8ML: Machine Learning-Augmented Density Functional Theory Nuclear Magnetic Resonance Computations for High-Throughput In Silico Solution Structure Validation and Revision of Complex Alkaloids. J Org Chem 2022; 87:4818-4828. [PMID: 35302771 DOI: 10.1021/acs.joc.2c00169] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Machine learning (ML) profoundly improves the accuracy of the fast DU8+ hybrid density functional theory/parametric computations of nuclear magnetic resonance spectra, allowing for high throughput in silico validation and revision of complex alkaloids and other natural products. Of nearly 170 alkaloids surveyed, 35 structures are revised with the next-generation ML-augmented DU8 method, termed DU8ML.
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Affiliation(s)
- Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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11
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Gan D, Zhu L, Zhang XR, Li CZ, Wang CY, Cai L, Ding ZT. Penaloidines A and B: two unprecedented pyridine alkaloids from Penicillium sp. KYJ-6. Org Chem Front 2022. [DOI: 10.1039/d1qo01879e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Penaloidines A (1) and B (2), a pair of epimers, unprecedented meroterpenoid pyridine alkaloids possessing a tetrahydrofuro[3,2-c][2,7]naphthyridinyl scaffold, were characterized from Penicillium sp. KYJ-6. Their structures were elucidated by spectroscopic...
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12
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Novitskiy IM, Kutateladze AG. DU8+ Computations Reveal a Common Challenge in the Structure Assignment of Natural Products Containing a Carboxylic Anhydride Moiety. J Org Chem 2021; 86:17511-17515. [PMID: 34743508 DOI: 10.1021/acs.joc.1c02291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DU8+ computations of NMR spectra revealed a relatively common error in the structure assignment of carboxylic anhydride-containing natural products. Computationally driven revisions of ten of these structures are reported in this Note. The majority of the misassigned structures featured a hydroxy group that is proximal to the proposed anhydride moiety and capable of lactone formation.
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Affiliation(s)
- Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
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13
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Recent Advances in Oxa-6π Electrocyclization Reactivity for the Synthesis of Privileged Natural Product Scaffolds. ORGANICS 2021. [DOI: 10.3390/org2040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The stunning advances in understanding the reactivity and selectivity principles of asymmetric pericyclic reactions have had a profound impact on the synthetic planning of complex natural products. Indeed, electrocyclizations, cycloadditions, and sigmatropic rearrangements enable synthetic chemists to craft highly functionalized scaffolds that would not otherwise be possible with a similar atom-, step-, and redox-economy. In this review, selected examples from the last two decades of research (2003–2020) on tandem processes combining oxa-6π electrocyclic reactions are discussed in terms of reactivity challenges, inherent reversibility, and key structural bond formation in the assembly of natural products. A particular emphasis is given to the electrocyclic ring-closures in the tandem processes featuring Knoevenagel-type condensations, Diels–Alder cycloadditions, Stille couplings, and oxidative dearomatizations. The synthetic manifolds reviewed here illustrate how oxa-6π electrocyclizations are intimately linked to the construction of complex natural product scaffolds and have inspired a number of biomimetic syntheses in the laboratory.
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14
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Zanardi MM, Sarotti AM. Sensitivity Analysis of DP4+ with the Probability Distribution Terms: Development of a Universal and Customizable Method. J Org Chem 2021; 86:8544-8548. [DOI: 10.1021/acs.joc.1c00987] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- María Marta Zanardi
- Instituto de Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, S2002QEO Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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15
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Nazarski RB. Summary of DFT calculations coupled with current statistical and/or artificial neural network (ANN) methods to assist experimental NMR data in identifying diastereomeric structures. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Yin F, Huan X, Mudianta IW, Miao Z, Wang H, Guo Y, Li X. Polyoxygenated Cembranoids from Soft Coral
Lobophytum Crassum
and Their Anti‐tumoral Activities. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fang‐Zhou Yin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi‐Tech Park Shanghai 201203 China
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals and College of Pharmaceutical Science, Zhejiang University of Technology Hangzhou Zhejiang 310014 China
| | - Xia‐Juan Huan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi‐Tech Park Shanghai 201203 China
| | - I. Wayan Mudianta
- Department of Chemistry, Universitas Pendidikan Ganesha Bali 81116 Indonesia
| | - Ze‐Hong Miao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi‐Tech Park Shanghai 201203 China
| | - Hong Wang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals and College of Pharmaceutical Science, Zhejiang University of Technology Hangzhou Zhejiang 310014 China
| | - Yue‐Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi‐Tech Park Shanghai 201203 China
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals and College of Pharmaceutical Science, Zhejiang University of Technology Hangzhou Zhejiang 310014 China
| | - Xu‐Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi‐Tech Park Shanghai 201203 China
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17
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Inose K, Tanaka S, Tanaka K, Hashimoto M. Cyclohelminthol CPs: Scope and Limitations of Density Functional Theory-Based Structural Elucidation of Natural Products. J Org Chem 2021; 86:1505-1515. [DOI: 10.1021/acs.joc.0c02378] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kota Inose
- Faculty of Agriculture and Bioscience, Hirosaki University, 3-Bunkyo-cho, Hirosaki 036-8561, Japan
| | - Shizuya Tanaka
- Faculty of Agriculture and Bioscience, Hirosaki University, 3-Bunkyo-cho, Hirosaki 036-8561, Japan
| | - Kazuaki Tanaka
- Faculty of Agriculture and Bioscience, Hirosaki University, 3-Bunkyo-cho, Hirosaki 036-8561, Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Bioscience, Hirosaki University, 3-Bunkyo-cho, Hirosaki 036-8561, Japan
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18
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Daranas AH, Sarotti AM. Are Computational Methods Useful for Structure Elucidation of Large and Flexible Molecules? Belizentrin as a Case Study. Org Lett 2020; 23:503-507. [PMID: 33382270 DOI: 10.1021/acs.orglett.0c04016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantum mechanical NMR methods are progressively becoming decisive in structure elucidation. However, problems arise using low-level calculations for complex molecules, whereas methods using higher levels of theory are not practical for large molecules. This report outlines a synergistic effort employing computationally inexpensive quantum mechanical NMR calculations with conformer selection incorporating 3JHH values as a way to solve the structure of large, complex, and highly flexible molecules using readily available computational resources with belizentrin as a case study.
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Affiliation(s)
- Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna 38206, Tenerife, Spain
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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19
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Structure elucidation of small organic molecules by contemporary computational chemistry methods. Arch Pharm Res 2020; 43:1114-1127. [DOI: 10.1007/s12272-020-01277-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
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20
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Vieira de Castro T, Yahiaoui O, Peralta RA, Fallon T, Lee V, George JH. Biomimetic Synthesis Enables the Structure Revision of Littordials E and F and Drychampone B. Org Lett 2020; 22:8161-8166. [DOI: 10.1021/acs.orglett.0c03156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Oussama Yahiaoui
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ricardo A. Peralta
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Thomas Fallon
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Victor Lee
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Jonathan H. George
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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21
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Li SW, Cuadrado C, Huan XJ, Yao LG, Miao ZH, Hernandez Daranas A, Guo YW. Rare new bicyclic cembranoid ethers and a novel trihydroxy prenylated guaiane from the Xisha soft coral Lobophytum sp. Bioorg Chem 2020; 103:104223. [DOI: 10.1016/j.bioorg.2020.104223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
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22
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Li HT, Duan RT, Liu T, Yang RN, Wang JP, Liu SX, Yang YB, Zhou H, Ding ZT. Penctrimertone, a bioactive citrinin dimer from the endophytic fungus Penicillium sp. T2-11. Fitoterapia 2020; 146:104711. [DOI: 10.1016/j.fitote.2020.104711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
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23
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Marcarino MO, Zanardi MM, Cicetti S, Sarotti AM. NMR Calculations with Quantum Methods: Development of New Tools for Structural Elucidation and Beyond. Acc Chem Res 2020; 53:1922-1932. [PMID: 32794691 DOI: 10.1021/acs.accounts.0c00365] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structural elucidation is an important and challenging stage in the discovery of new organic molecules. Single-crystal X-ray analysis provides the most unquestionable results, though in practice the availability of suitable crystals limits its broad use. On the other hand, NMR spectroscopy has become the leading and universal technique to accomplish the task. Despite continuous advances in the field, the misinterpretation of NMR data is commonplace, evidenced by the large number of erroneous structures being published in top journals. Quantum calculations of NMR chemical shifts and scalar coupling constants emerged as ideal complements to facilitate the elucidation process when experimental NMR data is inconclusive. Since seminal reports demonstrated that affordable DFT methods provide NMR predictions accurate enough to differentiate among closely related isomers, the discipline has experienced substantial growth. The impact has been felt in different areas, and nowadays the results of such calculations are routinely seen in high impact literature.This Account describes our investigations in the field of quantum NMR calculations, focusing on the development of tools for structural elucidation and practical applications. We pioneered the use of artificial intelligence methods in the development of novel strategies of structural validation. Our first generation of trained artificial neural networks (ANNs) showed excellent ability to identify mistakes at the atom connectivity level, whereas the use of multidimensional pattern recognition pushed the performance to the stereochemical limit. In a conceptually different approach, we developed DP4+, an updated version of the DP4 probability used to determine the most likely structure among two or more candidates when one set of experimental data is available. Increasing the level of theory in NMR calculations and including unscaled data in the formalism improved the performance of the method, further validated to settle the configuration of challenging motifs such as spiroepoxides or Mosher's derivatives. One of the limitations of DP4+ is related to the relatively large computational cost involved in obtaining DFT-optimized geometries, which led to the development of a fast variant including the valuable information provided by coupling constants (J-DP4 method).These tools were explored to suggest the most probable structure of controversial natural or unnatural products originally misassigned, with some predictions further validated by synthesis (as in the case of pseudorubriflordilactone B). The possibility of predicting the structure of a natural product without requiring authentic sample was investigated in collaboration with Prof. Pilli (UNICAMP, Brazil) in the computer-guided total synthesis and stereochemical revisions of several natural products. Despite these advances, there remain considerable challenges, such as the case of configurational assessment of polar systems featuring multiple intramolecular hydrogen bonding interactions because of the poor energy predictions provided by most DFT methods. In our latest work, we tackle this problem by averaging the results provided by randomly generated ensembles, paving the way for a new paradigm in quantum NMR-assisted structural elucidation.
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Affiliation(s)
- Maribel O. Marcarino
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Marı́a M. Zanardi
- Instituto de Ingenierı́a Ambiental, Quı́mica y Biotecnologı́a Aplicada (INGEBIO), Facultad de Quı́mica e Ingenierı́a del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Soledad Cicetti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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24
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Liu W, Niu S, Zhao Z, Yang S, Liu J, Li Y, Fang X. Divergent Synthesis of Bicyclo[3.2.1]octenes and Cyclohexenes via Catalytic Annulations of Nazarov Reagent and Vinyl 1,2-Diketones. Org Lett 2020; 22:7572-7576. [PMID: 32909760 DOI: 10.1021/acs.orglett.0c02763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bicyclo[3.2.1]octanes and related structures are unique units that widely exist in natural products, but the rapid and stereoselective construction of this skeleton is a challenging issue. We report the stereodivergent synthesis of bicyclo[3.2.1]octenes using Nazarov reagents and alkenyl 1,2-diketones with Brønsted base catalysis under mild conditions. Both stereoisomers of the bridged products can be obtained by tuning the reaction conditions, and cyclohexene product can also be selectively formed.
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Affiliation(s)
- Wenjun Liu
- State Key Laboratory of Structural Chemistry, and Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350100, China
| | - Shengtong Niu
- State Key Laboratory of Structural Chemistry, and Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350100, China
| | - Zhifei Zhao
- State Key Laboratory of Structural Chemistry, and Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350100, China
| | - Shuang Yang
- State Key Laboratory of Structural Chemistry, and Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350100, China
| | - Jinggong Liu
- Orthopedics Department, Guangdong Provincial Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Guangzhou 510120, China
| | - Yongjin Li
- Orthopedics Department, Guangdong Provincial Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Guangzhou 510120, China
| | - Xinqiang Fang
- State Key Laboratory of Structural Chemistry, and Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Fuzhou 350100, China
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25
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Maslovskaya LA, Savchenko AI, Krenske EH, Chow S, Holt T, Gordon VA, Reddell PW, Pierce CJ, Parsons PG, Boyle GM, Kutateladze AG, Williams CM. EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods. Chemistry 2020; 26:11862-11867. [PMID: 32864777 DOI: 10.1002/chem.202001884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.
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Affiliation(s)
- Lidia A Maslovskaya
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Andrei I Savchenko
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Sharon Chow
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208, USA
| | - Victoria A Gordon
- EcoBiotics Limited, PO Box 1, Yungaburra, 4884, Queensland, Australia
| | - Paul W Reddell
- EcoBiotics Limited, PO Box 1, Yungaburra, 4884, Queensland, Australia
| | - Carly J Pierce
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Peter G Parsons
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208, USA
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
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26
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Sarotti AM. In Silico Reassignment of (+)-Diplopyrone by NMR Calculations: Use of a DP4/J-DP4/DP4+/DIP Tandem to Revise Both Relative and Absolute Configuration. J Org Chem 2020; 85:11566-11570. [DOI: 10.1021/acs.joc.0c01563] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ariel M. Sarotti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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27
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De Vita S, Terracciano S, Bruno I, Chini MG. From Natural Compounds to Bioactive Molecules through NMR and
In Silico
Methodologies. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Simona De Vita
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Stefania Terracciano
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Ines Bruno
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone‐ 86090 Pesche (IS) Italy
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28
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Matsumoto M, Miura S, Tonouchi A, Hashimoto M. DFT-supported structure determination of gymunomitr-3(15)-en-4b,9b-diol. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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29
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Wang F, Sarotti AM, Jiang G, Huguet-Tapia JC, Zheng SL, Wu X, Li C, Ding Y, Cao S. Waikikiamides A-C: Complex Diketopiperazine Dimer and Diketopiperazine-Polyketide Hybrids from a Hawaiian Marine Fungal Strain Aspergillus sp. FM242. Org Lett 2020; 22:4408-4412. [PMID: 32433885 PMCID: PMC8904076 DOI: 10.1021/acs.orglett.0c01411] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Waikikiamides A-C (1-3), structurally complex diketopiperazine derivatives, and putative biogenic precursors, (+)-semivioxanthin (4), notoamide F (5), and (-)-notoamide A (6), were isolated from Aspergillus sp. FM242. 1 and 2, bearing a hendecacyclic ring system, represent a novel skeleton. 3 features the first unique heterodimer of two notoamide analogs with an N-O-C bridge. Compounds 1 and 3 exhibit antiproliferative activity with IC50 values in the range of 0.56 to 1.86 μM. The gene clusters mined from the sequenced genome support their putative biosynthetic pathways.
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Affiliation(s)
- Fuqian Wang
- Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 200 West Kawili Street, Hilo, Hawai'i 96720, United States
- Department of Pharmacy, Wuhan No. 1 Hospital, Wuhan No. 1 Hospital, Wuhan 430022, China
| | - Ariel M Sarotti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - José C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, United States
| | - Shao-Liang Zheng
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Xiaohua Wu
- Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 200 West Kawili Street, Hilo, Hawai'i 96720, United States
| | - Chunshun Li
- Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 200 West Kawili Street, Hilo, Hawai'i 96720, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Shugeng Cao
- Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 200 West Kawili Street, Hilo, Hawai'i 96720, United States
- Cancer Biology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, Hawai'i 96813, United States
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30
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Tan YP, Savchenko AI, Agnew-Francis KA, Boyle GM, Bernhardt PV, Fraser JA, Williams CM. Kalparinol, a Salvialane (Isodaucane) Sesquiterpenoid Derived from Native Australian Dysphania Species That Suggests a Putative Biogenetic Link to Zerumbone. JOURNAL OF NATURAL PRODUCTS 2020; 83:1473-1479. [PMID: 32302147 DOI: 10.1021/acs.jnatprod.9b01039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dysphania is a genus of plants endemic to the Australian continent, occurring primarily in arid and temperate zones. Despite their prevalence, very little in the way of phytochemical and/or bioactivity investigation of native Dysphania has been performed. Herein reported is the isolation and elucidation of (6E,9E)-zerumbone epoxide and a hitherto unreported isomer, (6Z,9E)-zerumbone epoxide, from D. kalpari. In addition, a novel isodaucane sesquiterepene, kalparinol, was isolated from both D. kalpari and D. rhadinostachya. The coisolation of the humulene and isodaucane skeletons, combined with the lack of any cadalane systems, could suggest an alternate novel biogenetic pathway originating from zerumbone, which is unlike any other proposals for the isodaucene system.
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Affiliation(s)
- Yuen Ping Tan
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Andrei I Savchenko
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Kylie A Agnew-Francis
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029 Queensland, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - James A Fraser
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
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31
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Li SW, Cuadrado C, Yao LG, Daranas AH, Guo YW. Quantum Mechanical–NMR-Aided Configuration and Conformation of Two Unreported Macrocycles Isolated from the Soft Coral Lobophytum sp.: Energy Calculations versus Coupling Constants. Org Lett 2020; 22:4093-4096. [DOI: 10.1021/acs.orglett.0c01155] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Song-Wei Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Li-Gong Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Antonio Hernandez Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555, Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
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32
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Holt TA, Reddy DS, Huple DB, West LM, Rodríguez AD, Crimmins MT, Kutateladze AG. The Discreet Structural Diversity of Briarellins: DU8+ Guided Multiple Structure Revisions Yielded Two Unknown Structural Types. J Org Chem 2020; 85:6201-6205. [PMID: 32323536 DOI: 10.1021/acs.joc.0c00555] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Briarellins, a subset of C2-C11 cyclized cembranoids, were proposed to contain a C3-C14 ether or lactone bridge, similar to asbestinins. However, the total synthesis of the proposed structure of briarellin J revealed a misassignment. We revisited briarellins, computationally, with the help of a recently developed hybrid DFT/parametric method, DU8+, and revised the structures of briarellin C14-C3 ε-lactones to new structural types containing either a C14-C11 or C14-C12 lactone bridge. The original structures of briarellin and asbestinin ethers were confirmed.
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Affiliation(s)
- Tina A Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Deepak B Huple
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Lyndon M West
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Abimael D Rodríguez
- Molecular Science Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, 00926, Puerto Rico
| | - Michael T Crimmins
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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33
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34
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Yaoita Y, Machida K. Misassigned Polyoxygenated Sterols and Reassignments of Their Structures. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20907724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This review will summarize the authors’ studies on the reassignments of structures of 9 natural polyoxygenated sterols (24 S)-24-ethylcholest-8-ene-3β,5α,6β,7α-tetrol (1), (24 S)-24-ethylcholest-8(14)-ene-3β,5α,6β,7α-tetrol (2), (22 E)-24-methylcholesta-8(14),22-diene-3β,5α,6β,7α-tetrol (3), 5β,6β-epoxy-(22 E)-ergosta-8,22-diene-3β,7β-diol (4), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14α-pentol (5), 3β,5α,6β,8β,14α-pentahydroxy-(22 E)-ergost-22-en-7-one (6), 5β,6β-epoxy-24-methylenecholesta-8,24(28)-diene-3β,7α,11α-triol (7), 6β-acetoxy-(22 E)-10α-ergosta-7,22-diene-3β,5α-diol (8), and 8α,9α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,14α-triol (9). The structures of 1 to 9 have been reassigned as (24 S)-5α,6α-epoxy-24-ethylcholest-8-ene-3β,7α-diol (16), (24 S)-5α,6α-epoxy-24-ethylcholest-8(14)-ene-3β,7α-diol (17), 5α,6α-epoxy-(22 E)-ergosta-8(14),22-diene-3β,7α-diol (13), 5α,6α-epoxy-(22 E)-ergosta-8,22-diene-3β,7α-diol (12), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14β-pentol (25), 5α,6α;8α,14α-diepoxy-3β-hydroxy-(22 E)-ergost-22-en-7-one (18), 5α,6α-epoxyergosta-8,24(28)-diene-3β,7α,11α-triol (21), 6β-acetoxy-(22 E)-ergosta-7,22-diene-3β,5α-diol (26), and 8α,14α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,9α-triol (28), respectively, from the results of careful reexamination of the published1H and13C NMR spectral data.
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Affiliation(s)
- Yasunori Yaoita
- Pharmaceutical Education Center, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Koichi Machida
- Pharmaceutical Education Center, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan
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35
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Yang XW, Grossman RB. Revision of the Structure of Hypatulone A by NMR, Computations, and Biosynthetic Considerations. Org Lett 2020; 22:760-763. [PMID: 31908165 DOI: 10.1021/acs.orglett.9b04666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Xing-Wei Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People’s Republic of China
| | - Robert B. Grossman
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
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36
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Polavarapu PL, Santoro E. Vibrational optical activity for structural characterization of natural products. Nat Prod Rep 2020; 37:1661-1699. [DOI: 10.1039/d0np00025f] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review presents the recent progress towards elucidating the structures of chiral natural products and applications using vibrational optical activity (VOA) spectroscopy.
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37
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Zanardi MM, Marcarino MO, Sarotti AM. Redefining the Impact of Boltzmann Analysis in the Stereochemical Assignment of Polar and Flexible Molecules by NMR Calculations. Org Lett 2019; 22:52-56. [DOI: 10.1021/acs.orglett.9b03866] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- María M. Zanardi
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Maribel O. Marcarino
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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38
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Arachchige KSA, Fahrenhorst-Jones T, Burns JM, Al-Fayaad HA, Behera JN, Rao CNR, Clegg JK, Williams CM. 1,4-Diazacubane crystal structure rectified as piperazinium. Chem Commun (Camb) 2019; 55:11751-11753. [PMID: 31513198 DOI: 10.1039/c9cc06272f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All 21 [n]-azacubanes are proposed by theoreticians to be stable, however, to-date only the synthesis of 1,4-diazacubane has been reported - as a Ni2+ templated Kagome metal organic framework (MOF). Described herein is the structural reassignment of this Kagome MOF on the basis of deducing the precise experimental procedure, and demonstrating that rather than the formation of 1,4-diazacubane, charge is balanced by disordered piperazinium cations across a twelve-fold symmetry site. Furthermore, quantum chemical calculations reveal that 1,4-diazacubane is unlikely to form under the reported conditions due to unfavorable enthalpies for select hypothetical reactions leading to such a product. This significant structure correction upholds the unconquered synthesis status quo of azacubane.
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Affiliation(s)
| | - Tyler Fahrenhorst-Jones
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Jed M Burns
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Hydar A Al-Fayaad
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Jogendra N Behera
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064, India and Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India and School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752 050, India
| | - C N R Rao
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064, India and Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Jack K Clegg
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
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Schuppe AW, Zhao Y, Liu Y, Newhouse TR. Total Synthesis of (+)-Granatumine A and Related Bislactone Limonoid Alkaloids via a Pyran to Pyridine Interconversion. J Am Chem Soc 2019; 141:9191-9196. [PMID: 31117671 DOI: 10.1021/jacs.9b04508] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the first total synthesis of (+)-granatumine A, a limonoid alkaloid with PTP1B inhibitory activity, in ten steps. Over the course of this study, two key methodological advances were made: a cost-effective procedure for ketone α,β-dehydrogenation using allyl-Pd catalysis, and a Pd-catalyzed protocol to convert epoxyketones to 1,3-diketones. The central tetrasubstituted pyridine is formed by a convergent Knoevenagel condensation and carbonyl-selective electrocyclization cascade, which was followed by a direct transformation of a 2 H-pyran to a pyridine. These studies have led to the structural revision of two members of this family.
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Affiliation(s)
- Alexander W Schuppe
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520-8107 , United States
| | - Yizhou Zhao
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520-8107 , United States
| | - Yannan Liu
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520-8107 , United States
| | - Timothy R Newhouse
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520-8107 , United States
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Kutateladze AG, Holt T, Reddy DS. Natural Products Containing the Oxetane and Related Moieties Present Additional Challenges for Structure Elucidation: A DU8+ Computational Case Study. J Org Chem 2019; 84:7575-7586. [DOI: 10.1021/acs.joc.9b01005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Andrei G. Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - D. Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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