1
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Martins LMOS, Souto FT, Hoye TR, Alvarenga ES. Deciphering molecular structures: NMR spectroscopy and quantum mechanical insights of halogenated 4H-Chromenediones. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:583-598. [PMID: 38557999 DOI: 10.1002/mrc.5445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/15/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
Sesquiterpene lactones (SL) represent a class of secondary metabolites found in the Asteraceae family, notable for their unique structures. The SL α-santonin (1) and its derivatives are worthy of mention due to their diverse biological properties. Additionally, 4H-chromenes and 4H-chromones are appealing frameworks holding the capability to be used as structural motifs for new drugs. Furthermore, unambiguous structural elucidation is crucial for developing novel compounds for diverse applications. In this context, it is common to find in the literature molecules erroneously assigned. Therefore, the use of quantum mechanical calculations to simulate NMR chemical shifts has emerged as a valuable strategy. In this work, we conceived the synthesis of two halogenated 4H-chromenediones derived from photosantonic acid (2), a photoproduct arising from irradiation of α-santonin (1) in the ultraviolet region. The structure of the chlorinated and brominated products was determined by NMR analysis, with the aid of quantum mechanical calculations at the B3LYP/6-311 + G(2d,p)//M062x/6-31 + G(d,p) level of theory. All analyses were in agreement and led to the assignment of the brominated 4H-chromene-2,7-dione as (3S,3aS,5aR,9bS)-5a-(2-bromopropan-2-yl)-3-methyl-3,3a,5,5a,8,9b-hexahydro-4H-furo[2,3-f]chromene-2,7-dione (11b) and of the chlorinated 4H-chromene-2,7-dione as (3S,3aS,5aR,9bS)-5a-(2-chloropropan-2-yl)-3-methyl-3,3a,5,5a,8,9b-hexahydro-4H-furo[2,3-f]chromene-2,7-dione (12b). The diastereoselectivities of the reactions were explained based on products and intermediates formation energy calculated using B3LYP/6-31 + G(d,p) as the level of theory. Structures 11b and 12b were identified as the thermodynamic and kinetic products of the reaction among all candidates. Consequently, the strategy utilized in this study is robust and successfully illustrates the use of quantum mechanical calculations in the structural elucidation of new compounds with potential applications as novel drugs or products.
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Affiliation(s)
- Lucas M O S Martins
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Chemistry Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Thomas R Hoye
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Elson S Alvarenga
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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2
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Lin B, Liu T, Luo T. Gold-catalyzed cyclization and cycloaddition in natural product synthesis. Nat Prod Rep 2024; 41:1091-1112. [PMID: 38456472 DOI: 10.1039/d3np00056g] [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: 03/09/2024]
Abstract
Covering: 2016 to mid 2023Transition metal catalysis, known for its remarkable capacity to expedite the assembly of molecular complexity from readily available starting materials in a single operation, occupies a central position in contemporary chemical synthesis. Within this landscape, gold-catalyzed reactions present a novel and versatile paradigm, offering robust frameworks for accessing diverse structural motifs. In this review, we highlighted a curated selection of publications in the past 8 years, focusing on the deployment of homogeneous gold catalysis in the ring-forming step for the total synthesis of natural products. These investigations are categorized based on the specific ring formations they engender, accentuating the prevailing gold-catalyzed methodologies applied to surmount intricate challenges in natural products synthesis.
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Affiliation(s)
- Boxu Lin
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Tianran Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Tuoping Luo
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
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3
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Cortés I, Sarotti AM. Road Map Toward Computer-Guided Total Synthesis of Natural Products. The Dysiherbol A Case Study: What if Serendipity Hadn't Intervened? J Org Chem 2023; 88:14156-14164. [PMID: 37728229 DOI: 10.1021/acs.joc.3c01738] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
We present a computational study inspired by the story of dysiherbol A, a natural product whose putative structure was found incorrect through synthesis by a completely fortuitous event. While the carbon connectivity and chemical environment between both structures remain similar, the real dysiherbol A has a different molecular weight than that reported for the natural product. Had the synthesis groups not been favored by fortune, it could be speculated that a substantial amount of time and effort would have been required to solve the structural puzzle. Within the realm of computer-guided total synthesis of natural products, the question arose whether a synthesis group could have in silico reassigned the structure before embarking on the experimental adventure. To address this query, we evaluated some state-of-the-art computational procedures based on their computational demand and ease of implementation for nonexpert users with basic skills in computational chemistry (including HOSE, CASCADE, ANN-PRA, ML-J-DP4, DP4, and DP4+). While discussing the strengths and limitations of these methods, this case study provides a roadmap of what could be done before venturing into complex and time-demanding total synthesis projects.
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Affiliation(s)
- Iván Cortés
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 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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4
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Hanif N, Dinelsa FF, Dwi Yanti H, Murni A, Tanaka J. Stereochemical determination of NMR chemical shifts in marine terpenoids, antheliol and sangiangol B, using DFT calculations. Nat Prod Res 2023; 37:3170-3176. [PMID: 36395185 DOI: 10.1080/14786419.2022.2147171] [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: 09/27/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
Stereochemical determination of the flexible trinor-guaiane sesquiterpenoid, antheliol (1a) and the flexible diterpenoid, sangiangol B (2a), isolated from a marine soft coral, Anthelia sp., was supported by quantum chemical calculations of NMR chemical shifts at DFT levels. The relative configuration of antheliol is now revealed, as 1S*, 4S*, 7S*, 10R* as in 1b, whereas sangiangol B (2c) has complete stereochemistry as 1S*, 7R*, 8R*, 10R*, 11R*, 12S*.
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Affiliation(s)
| | | | - Henny Dwi Yanti
- Tropical Biopharmaca Research Center, IPB University, Bogor, Indonesia
| | - Anggia Murni
- Tropical Biopharmaca Research Center, IPB University, Bogor, Indonesia
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Okinawa, Japan
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5
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Martorano LH, Brito JT, de Albuquerque ACF, Ribeiro CMR, Fiorot RG, Carneiro JWDM, Costa FLP, Valverde AL, Dos Santos Junior FM. Revisiting the structure of Heliannuol L: A computational approach. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:434-441. [PMID: 34741339 DOI: 10.1002/mrc.5230] [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: 09/29/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Recently, structural elucidation of natural products has undergone a revolution. The combined use of different modern spectroscopic methods has allowed obtaining a complete structural assignment of natural products using small amounts of sample. However, despite the extraordinary ongoing advances in spectroscopy, the mischaracterization of natural products has been and remains a recurrent problem, especially when the substance presents several stereogenic centers. The misinterpretation of nuclear magnetic resonance (NMR) data has resulted in frequent reports addressing structural reassignment. In this context, a great effort has been devoted to developing quantum chemical calculations that simulate NMR parameters accurately, allowing to achieve a more precise spectral interpretation. In this work, we employed a protocol for theoretical calculations of 1 H NMR chemical shifts and coupling constants using density functional theory (DFT), followed by the application of the DP4+ method to revisit the structure of Heliannuol L, a member of the Heliannuol class, isolated from Helianthus annuus. Our results indicate that the originally proposed structure of Heliannuol L needs a stereochemical reassignment, placing the hydroxyl bonded to C10 in the opposite side of the methyl and hydroxyl groups bonded to C7 and C8, respectively.
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Affiliation(s)
- Lucas H Martorano
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University (UFF), Niterói, Brazil
| | - Jordana T Brito
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University (UFF), Niterói, Brazil
| | | | - Carlos Magno Rocha Ribeiro
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University (UFF), Niterói, Brazil
| | - Rodolfo Goetze Fiorot
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University (UFF), Niterói, Brazil
| | | | | | - Alessandra L Valverde
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University (UFF), Niterói, Brazil
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6
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Cui Y, Lv J, Song T, Ren J, Wang Z. Highly efficient construction of an oxa-[3.2.1]octane-embedded 5-7-6 tricyclic carbon skeleton and ring-opening of the bridged ring via C-O bond cleavage. RSC Adv 2022; 12:9519-9523. [PMID: 35424922 PMCID: PMC8985103 DOI: 10.1039/d2ra01315k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
We report herein a highly efficient strategy for construction of a bridged oxa-[3.2.1]octane-embedded 5–7–6 tricyclic carbon skeleton through [3 + 2] IMCC (intramolecular [3 + 2] cross-cycloaddition), and the substituents and/or stereochemistries on C-4, C-6, C-7 and C-10 fully match those in the rhamnofolane, tigliane and daphnane diterpenoids. Furthermore, ring-opening of the bridged oxa-[3.2.1]octane via C–O bond cleavage was also successfully achieved. We reported a highly efficient construction of an oxa-[3.2.1]octane-embedded 5–7–6 tricyclic carbon skeleton with a full match of the substituents and stereochemistries on C-4/-6/-7/-10 with those in the rhamnofolane/tigliane/daphnane diterpenoids.![]()
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Affiliation(s)
- Yi Cui
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 PR China
| | - Jiayuan Lv
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 PR China
| | - Tianhang Song
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 PR China
| | - Jun Ren
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 PR China
| | - Zhongwen Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 PR China
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7
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Sara AA, Um-e-Farwa UEF, Saeed A, Kalesse M. Recent Applications of the Diels–Alder Reaction in the Synthesis of Natural Products (2017–2020). SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1532-4763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThe Diels–Alder reaction has long been established as an extremely useful procedure in the toolbox of natural product chemists. It tolerates a wide spectrum of building blocks of different complexity and degrees of derivatization, and enables the formation of six-membered rings with well-defined stereochemistry. In recent years, many total syntheses of natural products have been reported that rely, at some point, on the use of a [4+2]-cycloaddition step. Among classic approaches, several modifications of the Diels–Alder reaction, such as hetero-Diels–Alder reactions, dehydro-Diels–Alder reactions and domino-Diels–Alder reactions, have been employed to extend the scope of this process in the synthesis of natural products. Our short review covers applications of the Diels–Alder reaction in natural product syntheses between 2017 and 2020, as well as selected methodologies which are inspired by, or that can be used to access natural products.1 Introduction2 Syntheses from 20173 Syntheses from 20184 Syntheses from 20195 Syntheses from 20206 Conclusion
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Affiliation(s)
| | | | - Aamer Saeed
- Quaid-I-Azam University, Department of Chemistry
| | - Markus Kalesse
- Leibniz Universität Hannover, Institut für Organische Chemie
- Helmholtz Zentrum für Infektionsforschung (HZI)
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8
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Takeda K, Katsuta R, Yajima A, Ishigami K, Kuwahara S, Nukada T. Synthesis and DFT-NMR-guided structure revision of cremenolide. Nat Prod Res 2022; 37:1577-1582. [PMID: 35001745 DOI: 10.1080/14786419.2021.2023867] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The structure of an anti-plant pathogenic and plant growth-promoting nonenolide, namely cremenolide, was revised by an efficient combination of DFT-based theoretical NMR calculations and synthesis of a target diastereomer. Initially, the planar structure of cremenolide was reconsidered by an individual analysis of the reported NMR spectra. Subsequently, the relative configuration was predicted using NMR calculations of all possible diastereomers based on the ωB97X-D functional. Finally, the relative configuration of cremenolide was unambiguously confirmed by preparation of the proposed structure.
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Affiliation(s)
- Keita Takeda
- Department of Chemistry for Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan.,Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Ryo Katsuta
- Department of Chemistry for Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Arata Yajima
- Department of Chemistry for Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Ken Ishigami
- Department of Chemistry for Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Shigefumi Kuwahara
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tomoo Nukada
- Department of Chemistry for Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
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9
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de Oliveira MT, Alves JMA, Braga AAC, Wilson DJD, Barboza CA. Do Double-Hybrid Exchange-Correlation Functionals Provide Accurate Chemical Shifts? A Benchmark Assessment for Proton NMR. J Chem Theory Comput 2021; 17:6876-6885. [PMID: 34637284 DOI: 10.1021/acs.jctc.1c00604] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A benchmark density functional theory (DFT) study of 1H NMR chemical shifts for data sets comprising 200 chemical shifts, including complex natural products, has been carried out to assess the performance of DFT methods. Two new benchmark data sets, NMRH33 and NMRH148, have been established. The meta-GGA revTPSS performs remarkably well against the NMRH33 benchmark set (mean absolute deviation (MAD), 0.10 ppm; maximum deviation (max), 0.26 ppm) with the smallest MAD of all evaluated functionals. The best-performing double-hybrid density functional (DHDF), revDSD-BLYP (MAD, 0.16 ppm; max, 0.35 ppm), performs similarly to hybrid-GGA methods (e.g., mPW1PW91/6-311G(d) (MAD, 0.15 ppm; max, 0.36 ppm)), but at a considerably higher computational cost. The results indicate that currently available double-hybrid DFT methods offer no benefit over GGA (including hybrid and meta) functionals in the calculation of 1H NMR chemical shifts.
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Affiliation(s)
- Marcelo T de Oliveira
- Department of Chemistry and Physics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia.,Chemistry Institute of São Carlos, University of São Paulo, Avenida Trabalhador São Carlense 400, 13566-590 São Carlos, São Paulo, Brazil
| | - Júlia M A Alves
- Chemistry Institute of São Carlos, University of São Paulo, Avenida Trabalhador São Carlense 400, 13566-590 São Carlos, São Paulo, Brazil
| | - Ataualpa A C Braga
- Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
| | - David J D Wilson
- Department of Chemistry and Physics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Cristina A Barboza
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw 02-668, Poland
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10
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Wang M, Yin L, Cheng L, Yang Y, Li Y. Straightforward Stereoselective Synthesis of Seven-Membered Oxa-Bridged Rings through In Situ Generated Cycloheptenol Derivatives. J Org Chem 2021; 86:12956-12963. [PMID: 34436895 DOI: 10.1021/acs.joc.1c01648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An iodine-mediated stereoselective synthesis of seven-membered oxa-bridged rings via in situ generated cycloheptenols was reported. This process was realized through the combination of C-C σ-bond cleavage and C-O bond-forming reactions in a one-pot fashion from simple and easily accessible raw materials. The formation of carbon radicals initiated by I2 was the key to the reaction.
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Affiliation(s)
- Mengdan Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Liqiang Yin
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lu Cheng
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yajie Yang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yanzhong Li
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.,Key Laboratory of Polar Materials and Devices, Ministry of Education, 500 Dongchuan Road, Shanghai 200241, China
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11
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Marcarino MO, Cicetti S, Zanardi MM, Sarotti AM. A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide. Nat Prod Rep 2021; 39:58-76. [PMID: 34212963 DOI: 10.1039/d1np00030f] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.
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Affiliation(s)
- Maribel O Marcarino
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - Soledad Cicetti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - María M Zanardi
- Instituto de Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina.
| | - 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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12
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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13
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Gupta A, Chakraborty S, Ramakrishnan R. Revving up 13C NMR shielding predictions across chemical space: benchmarks for atoms-in-molecules kernel machine learning with new data for 134 kilo molecules. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abe347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
The requirement for accelerated and quantitatively accurate screening of nuclear magnetic resonance spectra across the small molecules chemical compound space is two-fold: (1) a robust ‘local’ machine learning (ML) strategy capturing the effect of the neighborhood on an atom’s ‘near-sighted’ property—chemical shielding; (2) an accurate reference dataset generated with a state-of-the-art first-principles method for training. Herein we report the QM9-NMR dataset comprising isotropic shielding of over 0.8 million C atoms in 134k molecules of the QM9 dataset in gas and five common solvent phases. Using these data for training, we present benchmark results for the prediction transferability of kernel-ridge regression models with popular local descriptors. Our best model, trained on 100k samples, accurately predicts isotropic shielding of 50k ‘hold-out’ atoms with a mean error of less than 1.9 ppm. For the rapid prediction of new query molecules, the models were trained on geometries from an inexpensive theory. Furthermore, by using a Δ-ML strategy, we quench the error below 1.4 ppm. Finally, we test the transferability on non-trivial benchmark sets that include benchmark molecules comprising 10–17 heavy atoms and drugs.
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14
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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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15
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Tabassum S, Zahoor AF, Ahmad S, Noreen R, Khan SG, Ahmad H. Cross-coupling reactions towards the synthesis of natural products. Mol Divers 2021; 26:647-689. [PMID: 33609222 DOI: 10.1007/s11030-021-10195-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/30/2021] [Indexed: 01/12/2023]
Abstract
Cross-coupling reactions are powerful synthetic tools for the formation of remarkable building blocks of many naturally occurring molecules, polymers and biologically active compounds. These reactions have brought potent transformations in chemical and pharmaceutical disciplines. In this review, we have focused on the use of cross-coupling reactions such as Suzuki, Negishi, Heck, Sonogashira and Stille in the total synthesis of some natural products of recent years (2016-2020). A short introduction of mentioned cross-coupling reactions along with highlighted aspects of natural products has been stated in separate sections. Additionally, few examples of natural products via incorporation of more than one type of cross-coupling reaction have also been added to demonstrate the importance of these reactions in organic synthesis.
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Affiliation(s)
- Shaheera Tabassum
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan.
| | - Sajjad Ahmad
- Department of Chemistry, University of Engineering and Technology, Lahore, Faisalabad Campus, Faisalabad, 38000, Pakistan
| | - Razia Noreen
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Samreen Gul Khan
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Hamad Ahmad
- Department of Chemistry, University of Management and Technology, Lahore, Pakistan
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16
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Costa FLP, de Albuquerque ACF, Fiorot RG, Lião LM, Martorano LH, Mota GVS, Valverde AL, Carneiro JWM, dos Santos Junior FM. Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights. Org Chem Front 2021. [DOI: 10.1039/d1qo00034a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.
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Affiliation(s)
| | - Ana C. F. de Albuquerque
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Rodolfo G. Fiorot
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Luciano M. Lião
- Instituto de Química
- Universidade Federal de Goiás
- 74690-900 Goiânia-GO
- Brazil
| | - Lucas H. Martorano
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Gunar V. S. Mota
- Faculdade de Ciências Naturais/Instituto de Ciências Exatas e Naturais
- Universidade Federal do Pará
- Belém-PA
- Brazil
| | - Alessandra L. Valverde
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - José W. M. Carneiro
- Departamento de Química Inorgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
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17
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Kawazoe R, Matsuo Y, Saito Y, Tanaka T. Computationally Assisted Structural Revision of Flavoalkaloids with a Seven-Membered Ring: Aquiledine, Isoaquiledine, and Cheliensisine. JOURNAL OF NATURAL PRODUCTS 2020; 83:3347-3353. [PMID: 33081470 DOI: 10.1021/acs.jnatprod.0c00691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aquiledine and cheliensisine are flavoalkaloids isolated from Aquilegia ecalcarata and Goniothalamus cheliensis, respectively. Different structures have been proposed for these flavoalkaloids; however, their 1H and 13C NMR spectroscopic data were virtually identical. In this study, the structures of aquiledine and cheliensisine were revised on the basis of the DFT calculation of NMR data including DP4+ and J-DP4 analysis, as well as specific rotations. Similarly, the structure of isoaquiledine, a regioisomer of aquiledine, was also revised. A biosynthetic pathway of these flavoalkaloids is proposed.
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Affiliation(s)
- Rina Kawazoe
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yosuke Matsuo
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yoshinori Saito
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Takashi Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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18
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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: 69] [Impact Index Per Article: 17.3] [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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19
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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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20
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Selvaraj K, Chauhan S, Sandeep K, Swamy KCK. Advances in [4+3]‐Annulation/Cycloaddition Reactions Leading to Homo‐ and Heterocycles with Seven‐Membered Rings. Chem Asian J 2020; 15:2380-2402. [DOI: 10.1002/asia.202000545] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/06/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Karuppu Selvaraj
- School of ChemistryUniversity of Hyderabad Hyderabad-500046 Telangana India
| | - Sachin Chauhan
- School of ChemistryUniversity of Hyderabad Hyderabad-500046 Telangana India
| | - K. Sandeep
- School of ChemistryUniversity of Hyderabad Hyderabad-500046 Telangana India
| | - K. C. Kumara Swamy
- School of ChemistryUniversity of Hyderabad Hyderabad-500046 Telangana India
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21
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Pinto BNS, Teixeira MG, Alvarenga ES. Synthesis and structural elucidation of a phthalide analog using NMR analysis and DFT calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:559-565. [PMID: 31774576 DOI: 10.1002/mrc.4976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Phtalides are secondary metabolites found in several fungi with a wide range of biological activities. A novel phthalide analog was synthesized by Diels-Alder reaction between cyclopentadiene and 3,4-dichlorofuran-2(5H)-one. Quantum mechanical calculations were used in conjunction with the spectrometric methods to determine the structure of the title compound. The calculated NMR chemical shifts for eight candidate pairs of enantiomers were compared with the experimental NMR chemical shifts applying the DP4 probability and mean absolute errors methodology. DP4 analysis using 1 H and 13 C NMR chemical shifts without assignment of the signals presented 100% probability for the correct candidate structure 3d, proving the consistency of the method even without spectra interpretation. Results from theoretical calculation and NMR spectra interpretation were in agreement to the structure of rac-(3aR,4S,4aS,5R,8S,8aR,9R,9aS)-3a,9a-dichloro-3a,4,4a,5,8,8a,9,9a-octahydro-4,9:5,8-dimethanonaphtho[2,3-c]furan-1(3H)-one.
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Affiliation(s)
- Bryan N S Pinto
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Milena G Teixeira
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elson S Alvarenga
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
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22
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Potmischil F, Hillebrand M, Kalchhauser H. Hydroacridines: Part 33. An experimental and DFT study of the 13 C NMR chemical shifts of the nitrosamines derived from the six stereoisomers of tetradecahydroacridine. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:249-259. [PMID: 31965644 DOI: 10.1002/mrc.4946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
The paper presents the experimental and DFT-calculated values of the 13 C NMR chemical shifts of the six stereoisomers of tetradecahydroacridine and of the corresponding nitrosamines. Performing the DFT calculations using several combinations of functional and basis sets, it was found that the best experimental-calculated agreement was obtained for OPBE/6-311++G (dp) method. Considering the effect of N-nitrosation upon the 13 C NMR chemical shifts of the C-α carbons of secondary amines, it was found that if following nitrosation both C-α carbons are shifted upfield or both are shifted downfield, then the resulted nitrosamine will have a sterically strained ─N═O group. If, however, one of the C-α is shifted upfield and the other is shifted downfield, then the ─N═O group will be strain-free or weakly strained. Our calculations predict strain energies of about 10-15 kcal mol-1 in the first case and ≈0-6 kcal mol-1 in the latter.
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Affiliation(s)
- Francisc Potmischil
- Department of Organic Chemistry, Biochemistry and Catalysis University of Bucharest, Romania
| | - Mihaela Hillebrand
- Department of Physical Chemistry, University of Bucharest, Bucharest, Romania
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23
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Navarro-Vázquez A. When not to rely on Boltzmann populations. Automated CASE-3D structure elucidation of hyacinthacines through chemical shift differences. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:139-144. [PMID: 31663628 DOI: 10.1002/mrc.4951] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/03/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
An Akaike Information Criterion (AIC) procedure (CASE-3D) has been successfully applied to the NMR based configurational assignment of reported hyacinthacines (1-3,5-8), recently target of configurational analysis using the popular DP4+ methodology. The present analysis makes use of reported 1 H and 13 C shifts and, in some particular cases, a few 3 JHH couplings. The difficulty in proper computational prediction of relative energies, in molecules capable of inter-molecular hydrogen bonding, introduces large errors in the prediction of conformationally averaged NMR properties in methods based on Boltzmann averaging such as DP4 or DP4+. In contrast CASE-3D conformational amplitudes are free parameters in the model. Here we show that the CASE-3D conformational model selection strategy, when combined with a larger energy cutoff in the molecular-modelling conformational exploration, was sufficient to correctly assign the relative configuration in five of seven cases. Introduction of more information, either by supplementing 1 H and 13 C data with a few J-couplings, or using a cutoff based on computed DFT energies for the definition of the conformational ensembles, allowed the safe assignment of configuration for all compounds.
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Affiliation(s)
- Armando Navarro-Vázquez
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco, Brazil, 50670-90.1
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24
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Martorano LH, Valverde AL, Ribeiro CMR, de Albuquerque ACF, Carneiro JWDM, Fiorot RG, M. dos Santos Junior F. Unraveling the helianane family: a complementary quantum mechanical study. NEW J CHEM 2020. [DOI: 10.1039/d0nj01396j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comprehensive work suggesting the amendment of helianane to the open ring curcudiol by means of computational spectroscopy and thermodynamic reasons.
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Affiliation(s)
- Lucas H. Martorano
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Alessandra L. Valverde
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Carlos Magno R. Ribeiro
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | | | - José Walkimar de M. Carneiro
- Department of Inorganic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Rodolfo G. Fiorot
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Fernando M. dos Santos Junior
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
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25
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Wright AC, Lee CW, Stoltz BM. Progress toward the Enantioselective Synthesis of Curcusones A-D via a Divinylcyclopropane Rearrangement Strategy. Org Lett 2019; 21:9658-9662. [PMID: 31763859 DOI: 10.1021/acs.orglett.9b03829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report our iterative efforts toward the divergent total syntheses of curcusones A-D via Suzuki coupling, intramolecular cyclopropanation, and a key divinylcyclopropane rearrangement. Progress of our synthesis was repeatedly challenged by the highly substrate-dependent cyclopropanation step, which we could ultimately overcome by judicious choice of substituents on the six-membered ring fragment.
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Affiliation(s)
- Austin C Wright
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering , California Institute of Technology , MC 101-20, Pasadena , California 91125 , United States
| | - Chung Whan Lee
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering , California Institute of Technology , MC 101-20, Pasadena , California 91125 , United States
| | - Brian M Stoltz
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering , California Institute of Technology , MC 101-20, Pasadena , California 91125 , United States
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26
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Drew MA, Arndt S, Richardson C, Rudolph M, Hashmi ASK, Hyland CJT. Divergent gold-catalysed reactions of cyclopropenylmethyl sulfonamides with tethered heteroaromatics. Chem Commun (Camb) 2019; 55:13971-13974. [PMID: 31686080 DOI: 10.1039/c9cc06241f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cyclopropenylmethyl sulfonamides with tethered heteroaromatics have been demonstrated to undergo divergent gold-catalysed cyclisation reactions. A formal dearomative (4+3) cycloaddition takes place with furan-tethered substrates, yielding densely functionalised 5,7-fused heterocycles related to the bioactive curcusone natural products. Indole-tethered substrates display divergent reactivity giving biologically important tetrahydro-β-carbolines via a Friedel-Crafts mechanism.
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Affiliation(s)
- Melanie A Drew
- School of Chemistry and Molecular Bioscience, and Molecular Horizons Research Institute, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia.
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27
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Grimblat N, Gavín JA, Hernández Daranas A, Sarotti AM. Combining the Power of J Coupling and DP4 Analysis on Stereochemical Assignments: The J-DP4 Methods. Org Lett 2019; 21:4003-4007. [DOI: 10.1021/acs.orglett.9b01193] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolás Grimblat
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, República Argentina
| | - José A. Gavín
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, 38206 Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, 38206 Tenerife, Spain
- Instituto de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - 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, República Argentina
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28
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Zhang J, Liao Z, Chen L, Zhu S. Rapid Access to Oxa‐Bridged Bicyclic Skeletons through Gold‐Catalyzed Tandem Rearrangement Reaction. Chemistry 2019; 25:9405-9409. [DOI: 10.1002/chem.201900807] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/12/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Jiantao Zhang
- Key Laboratory of Functional Molecular Engineering of, Guangdong ProvinceSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510640 P. R. China
| | - Zhehui Liao
- Key Laboratory of Functional Molecular Engineering of, Guangdong ProvinceSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510640 P. R. China
| | - Lianfen Chen
- Key Laboratory of Functional Molecular Engineering of, Guangdong ProvinceSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510640 P. R. China
| | - Shifa Zhu
- Key Laboratory of Functional Molecular Engineering of, Guangdong ProvinceSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510640 P. R. China
- Guangdong Engineering Research Center for Green Fine ChemicalsSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510640 P. R. China
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29
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Zanardi MM, Sortino MA, Sarotti AM. On the effect of intramolecular H-bonding in the configurational assessment of polyhydroxylated compounds with computational methods. The hyacinthacines case. Carbohydr Res 2019; 474:72-79. [DOI: 10.1016/j.carres.2019.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 01/04/2023]
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30
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Ariai J, Saielli G. "Through-Space" Relativistic Effects on NMR Chemical Shifts of Pyridinium Halide Ionic Liquids. Chemphyschem 2019; 20:108-115. [PMID: 30312005 DOI: 10.1002/cphc.201800955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 12/27/2022]
Abstract
We have investigated, using two-component relativistic density functional theory (DFT) at ZORA-SO-BP86 and ZORA-SO-PBE0 level, the occurrence of relativistic effects on the 1 H, 13 C, and 15 N NMR chemical shifts of 1-methylpyridinium halides [MP][X] and 1-butyl-3-methylpyridinium trihalides [BMP][X3 ] ionic liquids (ILs) (X=Cl, Br, I) as a result of a non-covalent interaction with the heavy anions. Our results indicate a sizeable deshielding effect in ion pairs when the anion is I- and I3 - . A smaller, though nonzero, effect is observed also with bromine while chlorine based anions do not produce an appreciable relativistic shift. The chemical shift of the carbon atoms of the aromatic ring shows an inverse halogen dependence that has been rationalized based on the little C-2s orbital contribution to the σ-type interaction between the cation and anion. This is the first detailed account and systematic theoretical investigation of a relativistic heavy atom effect on the NMR chemical shifts of light atoms in the absence of covalent bonds. Our work paves the way and suggests the direction for an experimental investigation of such elusive signatures of ion pairing in ILs.
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Affiliation(s)
- Jama Ariai
- Department of Chemical Sciences University of Padova, Via Marzolo 1, 35131, Padua, Italy.,Present address: Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Giacomo Saielli
- CNR Institute on Membrane Technology, Padova Unit, Via Marzolo 1, 35131, Padua, Italy
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31
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Li YL, Zhu RX, Li G, Wang NN, Liu CY, Zhao ZT, Lou HX. Secondary metabolites from the endolichenic fungus Ophiosphaerella korrae. RSC Adv 2019; 9:4140-4149. [PMID: 35520149 PMCID: PMC9060614 DOI: 10.1039/c8ra10329a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/12/2019] [Indexed: 12/28/2022] Open
Abstract
The isolation of the cytotoxic fractions from the endolichenic fungus Ophiosphaerella korrae yielded six new metabolites, including five polyketides (ophiofuranones A (1) and B (2), with unusual furopyran-3,4-dione-fused heterocyclic skeletons, ophiochromanone (3), ophiolactone (4), and ophioisocoumarin (5)), one sesquiterpenoid ophiokorrin (10), and nine known compounds. Their structures were established on the basis of the analysis of HRESIMS and NMR spectroscopic data. ECD calculations, GIAO NMR shift calculations and single-crystal X-ray diffraction were employed for the stereo-structure determination. A plausible biogenetic pathway for the ophiofuranones A (1) and B (2) was proposed. The cytotoxic assay suggested that the five known perylenequinones mainly contributed to the cytoxicity of the extract. Further phytotoxic studies indicated that ophiokorrin inhibited root elongation in the germination of Arabidopsis thaliana with an IC50 value of 18.06 μg mL−1. Six new metabolites were isolated from the endolichenic fungus Ophiosphaerella korrae. Ophiokorrin inhibited root elongation in the germination of Arabidopsis thaliana.![]()
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Affiliation(s)
- Yue-Lan Li
- Department of Natural Product Chemistry
- Key Lab of Chemical Biology (MOE)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan 250012
| | - Rong-Xiu Zhu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- People's Republic of China
| | - Gang Li
- Department of Natural Medicinal Chemistry and Pharmacognosy
- School of Pharmacy
- Qingdao University
- Qingdao 266021
- People's Republic of China
| | - Ning-Ning Wang
- Department of Natural Product Chemistry
- Key Lab of Chemical Biology (MOE)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan 250012
| | - Chun-Yu Liu
- Department of Natural Product Chemistry
- Key Lab of Chemical Biology (MOE)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan 250012
| | - Zun-Tian Zhao
- College of Life Sciences
- Shandong Normal University
- Jinan 250014
- People's Republic of China
| | - Hong-Xiang Lou
- Department of Natural Product Chemistry
- Key Lab of Chemical Biology (MOE)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan 250012
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32
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Abstract
We investigate by explicit parameter optimization to what extent basis sets of polarized double-ζ quality can introduce compensating errors in five different density functional methods. It is shown that minor changes in the contraction coefficients of the valence functions in the basis sets can have a significant impact and allow different density functional methods to achieve very similar performances. This holds for nuclear magnetic shielding constants and for isomerization energies, barrier heights, and noncovalent interactions. It is furthermore shown that errors due to neglect of vibrational and solvent effects can be absorbed in the combined method and basis set errors. These findings hold for data sets consisting of 50-150 data points. This raises the question of whether the common practice of identifying combinations of density functional methods and basis sets that have a good performance against a selected set of reference data should be considered as data fitting in the combined parameter space spanned by the method and basis set.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry , Aarhus University , DK-8000 Aarhus , Denmark
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33
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Saielli G. Computational Spectroscopy of Ionic Liquids for Bulk Structure Elucidation. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Giacomo Saielli
- CNR Institute on Membrane Technology; Unit of Padova; Via Marzolo 1-35131 Padova Italy
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
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34
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Betterley NM, Kerdphon S, Chaturonrutsamee S, Kongsriprapan S, Surawatanawong P, Soorukram D, Pohmakotr M, Andersson PG, Reutrakul V, Kuhakarn C. Bi(OTf)3
Enabled C-F Bond Cleavage in HFIP: Electrophilic Aromatic Formylation with Difluoro(phenylsulfanyl)methane. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201800313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nolan M. Betterley
- Department of Chemistry and Center of Excellence, for Innovation in Chemistry (PERCH-CIC); Faculty of Science; Mahidol University; Rama 6 Road Bangkok 10400 Thailand
| | - Sutthichat Kerdphon
- Department of Organic Chemistry; Stockholm University, Arrhenius-laboratory; 10691 Stockholm Sweden
| | - Suppisak Chaturonrutsamee
- Department of Chemistry and Center of Excellence, for Innovation in Chemistry (PERCH-CIC); Faculty of Science; Mahidol University; Rama 6 Road Bangkok 10400 Thailand
- Research and Development Department; International Laboratories Corp., Ltd. Bang Pli; Samut Prakan 10540 Thailand
| | - Sopanat Kongsriprapan
- Faculty of Science at Si Racha; Kasetsart University; Si Racha Campus Chonburi Thailand
| | - Panida Surawatanawong
- Department of Chemistry and Center of Excellence, for Innovation in Chemistry (PERCH-CIC); Faculty of Science; Mahidol University; Rama 6 Road Bangkok 10400 Thailand
| | - Darunee Soorukram
- Department of Chemistry and Center of Excellence, for Innovation in Chemistry (PERCH-CIC); Faculty of Science; Mahidol University; Rama 6 Road Bangkok 10400 Thailand
| | - Manat Pohmakotr
- Department of Chemistry and Center of Excellence, for Innovation in Chemistry (PERCH-CIC); Faculty of Science; Mahidol University; Rama 6 Road Bangkok 10400 Thailand
| | - Pher G. Andersson
- Department of Organic Chemistry; Stockholm University, Arrhenius-laboratory; 10691 Stockholm Sweden
| | - Vichai Reutrakul
- Department of Chemistry and Center of Excellence, for Innovation in Chemistry (PERCH-CIC); Faculty of Science; Mahidol University; Rama 6 Road Bangkok 10400 Thailand
| | - Chutima Kuhakarn
- Department of Chemistry and Center of Excellence, for Innovation in Chemistry (PERCH-CIC); Faculty of Science; Mahidol University; Rama 6 Road Bangkok 10400 Thailand
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35
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Navarro-Vázquez A, Gil RR, Blinov K. Computer-Assisted 3D Structure Elucidation (CASE-3D) of Natural Products Combining Isotropic and Anisotropic NMR Parameters. JOURNAL OF NATURAL PRODUCTS 2018; 81:203-210. [PMID: 29323895 DOI: 10.1021/acs.jnatprod.7b00926] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A computer-assisted structural elucidation (CASE-3D) strategy based on the use of isotropic and/or anisotropic NMR data is proposed to elucidate relative configuration and preferred conformation in complex natural products. The methodology involves the selection of conformational models through the use of the Akaike Information Criterion and scoring of the different configurations. As illustrative examples, the methodology furnished the correct configuration of the already known compounds artemisinin (1) and homodimericin A (2). Revised structures (5 and 6), including their absolute configuration, for the recently reported curcusones I (3) and J (4) are proposed.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco , Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Kirill Blinov
- MestReLab Research S. L. Feliciano Barrera , 9 Baixo, Santiago de Compostela, A Coruña, 15706 Spain
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36
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Yin Z, He Y, Chiu P. Application of (4+3) cycloaddition strategies in the synthesis of natural products. Chem Soc Rev 2018; 47:8881-8924. [DOI: 10.1039/c8cs00532j] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review summarizes the applications of (4+3) cycloadditions, both classical and formal, in the syntheses of natural products in the last two decades.
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Affiliation(s)
- Zengsheng Yin
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- P. R. China
| | - Yun He
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- P. R. China
| | - Pauline Chiu
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- P. R. China
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