1
|
Vang ZP, Sonstrom RE, Scolati HN, Clark JR, Pate BH. Assignment of the absolute configuration of molecules that are chiral by virtue of deuterium substitution using chiral tag molecular rotational resonance spectroscopy. Chirality 2023; 35:856-883. [PMID: 37277968 PMCID: PMC11102577 DOI: 10.1002/chir.23596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 06/07/2023]
Abstract
Chiral tag molecular rotational resonance (MRR) spectroscopy is used to assign the absolute configuration of molecules that are chiral by virtue of deuterium substitution. Interest in the improved performance of deuterated active pharmaceutical ingredients has led to the development of precision deuteration reactions. These reactions often generate enantioisotopomer reaction products that pose challenges for chiral analysis. Chiral tag rotational spectroscopy uses noncovalent derivatization of the enantioisotopomer to create the diastereomers of the 1:1 molecular complexes of the analyte and a small, chiral molecule. Assignment of the absolute configuration requires high-confidence determinations of the structures of these weakly bound complexes. A general search method, CREST, is used to identify candidate geometries. Subsequent geometry optimization using dispersion corrected density functional theory gives equilibrium geometries with sufficient accuracy to identify the isomers of the chiral tag complexes produced in the pulsed jet expansion used to introduce the sample into the MRR spectrometer. Rotational constant scaling based on the fact that the diastereomers have the same equilibrium geometry gives accurate predictions allowing identification of the homochiral and heterochiral tag complexes and, therefore, assignment of absolute configuration. The method is successfully applied to three oxygenated substrates from enantioselective Cu-catalyzed alkene transfer hydrodeuteration reaction chemistry.
Collapse
Affiliation(s)
- Zoua Pa Vang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Reilly E. Sonstrom
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
- BrightSpec Inc, Charlottesville, Virginia, USA
| | - Haley N. Scolati
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Joseph R. Clark
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Brooks H. Pate
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
2
|
Franco BA, Luciano ER, Sarotti AM, Zanardi MM. DP4+App: Finding the Best Balance between Computational Cost and Predictive Capacity in the Structure Elucidation Process by DP4+. Factors Analysis and Automation. JOURNAL OF NATURAL PRODUCTS 2023; 86:2360-2367. [PMID: 37721602 DOI: 10.1021/acs.jnatprod.3c00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
DP4+ is one of the most popular methods for the structure elucidation of natural products using NMR calculations. While the method is simple and easy to implement, it requires a series of procedures that can be tedious, coupled with the fact that its computational demand can be high in certain cases. In this work, we made a substantial improvement to these limitations. First, we deeply explored the effect of molecular mechanics architecture on the DP4+ formalism (MM-DP4+). In addition, a Python applet (DP4+App) was developed to automate the entire process, requiring only the Gaussian NMR output files and a spreadsheet containing the experimental NMR data and labels. The script is designed to use the statistical parameters from the original 24 levels of theory (employing B3LYP/6-31G* geometries) and the new 36 levels explored in this work (over MMFF geometries). Furthermore, it enables the development of customizable methods using any desired level of theory, allowing for a free choice of test molecules.
Collapse
Affiliation(s)
- Bruno A Franco
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Ezequiel R Luciano
- Instituto de Investigaciones en 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
| | - María M Zanardi
- Instituto de Investigaciones en Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| |
Collapse
|
3
|
Jagora A, Szwarc S, Litaudon M, Dumontet V, Gallard JF, Beniddir MA, Le Pogam P. Structure elucidation of an aspidofractinine-type monoterpene indole alkaloid from Melodinus reticulatus. Z NATURFORSCH C 2023; 78:271-274. [PMID: 36793235 DOI: 10.1515/znc-2022-0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/26/2023] [Indexed: 02/17/2023]
Abstract
The structure and complete NMR assignments of aspidoreticulofractine, an aspidofractinine N-oxide, are reported. Its structure was elucidated based on a combination of spectroscopic techniques including 1D and 2D NMR, high-resolution mass spectrometry, and electronic circular dichroism.
Collapse
Affiliation(s)
- Adrien Jagora
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, 17, avenue des Sciences, 91400, Orsay, France
| | - Sarah Szwarc
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, 17, avenue des Sciences, 91400, Orsay, France
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Vincent Dumontet
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Mehdi A Beniddir
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, 17, avenue des Sciences, 91400, Orsay, France
| | - Pierre Le Pogam
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, 17, avenue des Sciences, 91400, Orsay, France
| |
Collapse
|
4
|
Naseem M, Asghar S, Farooq U, Lakhani A, Altaf Y, Hashmi MA. Determination of the Absolute Configuration of Ballonigrin Lactone A Using Density Functional Theory Calculations. ACS OMEGA 2023; 8:1923-1928. [PMID: 36687041 PMCID: PMC9850775 DOI: 10.1021/acsomega.2c03858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
We report the determination of the absolute configuration of a diterpenoid, namely, ballonigrin lactone A (BLA), by comparison of the computed optical rotations, [α]D, of its two diastereomers using density functional theory (DFT) calculations to the experimental [α]D value of +22.4. One of the diastereomers having configurations 4S, 5R, 6S, 10S, 15S was named "α-BLA," and the other one with configuration 4S, 5R, 6S, 10S, 15R was called "β-BLA". Six conformers for each diastereomer (α-BLA and β-BLA) of BLA were identified through their conformational analysis. [α]D values of these six conformations for each diastereomer were calculated using DFT at the mPW1PW91/6-311G(d,p)/SMDChloroform level of theory, leading to the conformationally averaged [α]D values of -96.8 for α-BLA and +65.1 for β-BLA. Thus, it was found that the experimental [α]D value of +22.4 was of 4S, 5R, 6S, 10S, 15R, i.e., β-BLA. Experimental and computed nuclear magnetic resonance (NMR) data were also compared, and this comparison was in accordance with the conclusion drawn from the comparison of [α]D values. Finally, the results were augmented with the calculation of the DP4 analysis, and the probability obtained also endorsed our earlier calculations.
Collapse
Affiliation(s)
- Misbah Naseem
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| | - Saleha Asghar
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| | - Umar Farooq
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, 22060 Abbottabad, Pakistan
| | - Ahmed Lakhani
- Department
of Biomedical and Health Sciences, Calumet
College of St. Joseph, 2400, New York Avenue, Whiting, Indiana 46394, United States
| | - Yasir Altaf
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| | - Muhammad Ali Hashmi
- Department
of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| |
Collapse
|
5
|
Zhang P, Zou JB, An Q, Yi P, Yuan CM, Huang LJ, Gu W, Hu ZX, Hao XJ. Two new cytisine-type alkaloids from the seeds of Thermopsis lanceolata. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2022; 24:1141-1149. [PMID: 34984943 DOI: 10.1080/10286020.2021.2020759] [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: 10/12/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Two new (1 and 2) cytisine-type alkaloids that were chemically inseparable isomers (present in a 1:1 ratio) were identified from the seeds of Thermopsis lanceolata R. Br. Their structures were elucidated by comprehensive spectroscopic data analysis (IR, UV, NMR, HRESIMS) and ECD calculation. Compound 1 displayed significant anti-tobacco mosaic virus (TMV) activity, while compounds 1 and 2 displayed moderate insecticidal activities against Aphis fabae with LC50 value of 43.15 and 46.47 mg/L, respectively.
Collapse
Affiliation(s)
- Peng Zhang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Ji-Bin Zou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Qiao An
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Ping Yi
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Chun-Mao Yuan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Lie-Jun Huang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Wei Gu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Zhan-Xing Hu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Xiao-Jiang Hao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
| |
Collapse
|
6
|
Otogo N'Nang E, Gallard JF, Champy P, Le Pogam P, Beniddir MA. Density functional theory-nuclear magnetic resonance-validated full structure elucidation of theionbrunonine C, an unstable N-oxide theionbrunonine from Mostuea brunonis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:1178-1184. [PMID: 35368097 DOI: 10.1002/mrc.5271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
The structure elucidation of theionbrunonine C, a thioether-bridged dimeric monoterpene indole alkaloid (MIA), and more generally, one of the very few sulfur-containing MIA, is reported after its isolation from Mostuea brunonis (Gelsemiaceae). This unstable structure had already been targeted for isolation in our former, molecular network-guided, investigation of this plant, but this compound had degraded before sufficient spectroscopic data could have been acquired for a complete structure assignment. With this constraint in mind, the rapid acquisition of nuclear magnetic resonance (NMR) data enabled retrieving sufficient spectroscopic information for full structure elucidation, although from a partial set of spectroscopic information (1 H and 13 C NMR; COSY, HSQC, and HMBC). In conjunction with biosynthetic considerations, the cursory examination of 13 C NMR data unambiguously defined the complete stereostructure of 1, as further supported by density functional theory (DFT)-NMR calculations and subsequent DP4 probability score.
Collapse
Affiliation(s)
- Elvis Otogo N'Nang
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
- Laboratoire de chimie des substances naturelles, Département Science Fondamentale de l'Ingénieur (INSAB), Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS, ICSN UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Champy
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Pierre Le Pogam
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Équipe "Chimie des substances naturelles" BioCIS, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2 N-1 Diastereomers. JOURNAL OF NATURAL PRODUCTS 2022; 85:1837-1849. [PMID: 35820115 DOI: 10.1021/acs.jnatprod.2c00427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.
Collapse
Affiliation(s)
- Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar- und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| |
Collapse
|
9
|
Huo ZQ, Zhu F, Zhang XW, Zhang X, Liang HB, Yao JC, Liu Z, Zhang GM, Yao QQ, Qin GF. Approaches to Configuration Determinations of Flexible Marine Natural Products: Advances and Prospects. Mar Drugs 2022; 20:333. [PMID: 35621984 PMCID: PMC9143581 DOI: 10.3390/md20050333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Flexible marine natural products (MNPs), such as eribulin and bryostatin, play an important role in the development of modern marine drugs. However, due to the multiple chiral centers and geometrical uncertainty of flexible systems, configuration determinations of flexible MNPs face great challenges, which, in turn, have led to obstacles in druggability research. To resolve this issue, the comprehensive use of multiple methods is necessary. Additionally, configuration assignment methods, such as X-ray single-crystal diffraction (crystalline derivatives, crystallization chaperones, and crystalline sponges), NMR-based methods (JBCA and Mosher's method), circular dichroism-based methods (ECCD and ICD), quantum computational chemistry-based methods (NMR calculations, ECD calculations, and VCD calculations), and chemical transformation-based methods should be summarized. This paper reviews the basic principles, characteristics, and applicability of the methods mentioned above as well as application examples to broaden the research and applications of these methods and to provide a reference for the configuration determinations of flexible MNPs.
Collapse
Affiliation(s)
- Zong-Qing Huo
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Feng Zhu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Xing-Wang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiao Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Hong-Bao Liang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Jing-Chun Yao
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Zhong Liu
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| | - Gui-Min Zhang
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Qing-Qiang Yao
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China;
| | - Guo-Fei Qin
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Lunan Pharmaceutical Group Co., Ltd., Linyi 273400, China; (Z.-Q.H.); (F.Z.); (H.-B.L.); (J.-C.Y.); (Z.L.); (G.-M.Z.)
| |
Collapse
|
10
|
Howarth A, Goodman JM. The DP5 probability, quantification and visualisation of structural uncertainty in single molecules. Chem Sci 2022; 13:3507-3518. [PMID: 35432857 PMCID: PMC8943899 DOI: 10.1039/d1sc04406k] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Whenever a new molecule is made, a chemist will justify the proposed structure by analysing the NMR spectra. The widely-used DP4 algorithm will choose the best match from a series of possibilities, but draws no conclusions from a single candidate structure. Here we present the DP5 probability, a step-change in the quantification of molecular uncertainty: given one structure and one 13C NMR spectra, DP5 gives the probability of the structure being correct. We show the DP5 probability can rapidly differentiate between structure proposals indistinguishable by NMR to an expert chemist. We also show in a number of challenging examples the DP5 probability may prevent incorrect structures being published and later reassigned. DP5 will prove extremely valuable in fields such as discovery-driven automated chemical synthesis and drug development. Alongside the DP4-AI package, DP5 can help guide synthetic chemists when resolving the most subtle structural uncertainty. The DP5 system is available at https://github.com/Goodman-lab/DP5.
Collapse
Affiliation(s)
- Alexander Howarth
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jonathan M Goodman
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|
11
|
Martins LMOS, Santos JO, Hoye T, Alvarenga ES. Synthesis of a novel naphthalenone endoperoxide and structural elucidation by nuclear magnetic resonance spectroscopy and theoretical calculation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:139-147. [PMID: 34265119 DOI: 10.1002/mrc.5195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/11/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Sesquiterpene lactones are found in plants of Asteraceae family, and endoperoxides are known for their antimalarial activity. Structural elucidation is a relevant aspect; however, it is not uncommon to find incorrect or incomplete structural assignments in the literature. Calculations based in quantum mechanics are frequently used to compute 1 H and 13 C NMR chemical shifts, and after comparing with the experimental data, the correct structure is established from diverse candidates. Targeting the synthesis of bioactive compounds, we envisaged the synthesis of a novel endoperoxide from the natural sesquiterpene lactone α-santonin (2). Photochemical transformation of α-santonin (2) to mazdasantonin (4) followed by photooxidation catalyzed by rose bengal afforded the novel endoperoxide 5. This new endoperoxide contains five stereogenic centers and is analogous to the antimalarial agent artemisinin (1). The relative configuration of the stereogenic centers of the endoperoxide were established by nuclear magnetic resonance (NMR) analyses and confirmed by theoretical calculations. All approaches were in complete agreement, and the structure of mazdasantonin endoperoxide was established as (3S,3aS,5aS,8R,9bS)-3,6,6-trimethyl-3,3a,4,5,8,9b-hexahydro-2H-5a,8-epidioxynaphtho[1,2-b]furan-2,7(6H)-dione.
Collapse
Affiliation(s)
| | - Juliana O Santos
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Thomas Hoye
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Elson S Alvarenga
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| |
Collapse
|
12
|
Semenov VA, Krivdin LB. Computational NMR of natural products. RUSSIAN CHEMICAL REVIEWS 2022. [DOI: 10.1070/rcr5027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
13
|
Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: Gibbs Sampling and Bayesian Inference Using Floating Chirality Distance Geometry Calculations. Mar Drugs 2021; 20:14. [PMID: 35049868 PMCID: PMC8781118 DOI: 10.3390/md20010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
Floating chirality restrained distance geometry (fc-rDG) calculations are used to directly evolve structures from NMR data such as NOE-derived intramolecular distances or anisotropic residual dipolar couplings (RDCs). In contrast to evaluating pre-calculated structures against NMR restraints, multiple configurations (diastereomers) and conformations are generated automatically within the experimental limits. In this report, we show that the "unphysical" rDG pseudo energies defined from NMR violations bear statistical significance, which allows assigning probabilities to configurational assignments made that are fully compatible with the method of Bayesian inference. These "diastereomeric differentiabilities" then even become almost independent of the actual values of the force constants used to model the restraints originating from NOE or RDC data.
Collapse
Affiliation(s)
- Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar-und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany;
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| |
Collapse
|
14
|
Souto JA, Román D, Domínguez M, Lera ÁR. Synthetic Studies on Alotamide A: Construction of
N
‐Demethylalotamide A. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101104] [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)
- José A. Souto
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| | - David Román
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| | - Marta Domínguez
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| | - Ángel R. Lera
- CINBIO Universidade de Vigo Departamento de Química Orgánica 36310 Vigo España
| |
Collapse
|
15
|
Hu ZX, Zou JB, An Q, Yi P, Yuan CM, Gu W, Huang LJ, Lou HY, Zhao LH, Hao XJ. Anti-tobacco mosaic virus (TMV) activity of chemical constituents from the seeds of Sophora tonkinensis. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2021; 23:644-651. [PMID: 33583289 DOI: 10.1080/10286020.2021.1886089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Two new compounds, including one new arylbenzofuran (1) and one new pterocarpanoid (2), along with nine known ones, were isolated from the seeds of Sophora tonkinensis. The structures of the new compounds were elucidated based on a comprehensive spectroscopic data analysis. Compounds 2 and 3 exhibited good anti-tobacco mosaic virus (TMV) activities with the protective inhibition rate of 69.62% and 68.72% respectively, at concentration of 100 μg/ml.
Collapse
Affiliation(s)
- Zhan-Xing Hu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Ji-Bin Zou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Qiao An
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Ping Yi
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Chun-Mao Yuan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Wei Gu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Lie-Jun Huang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Hua-Yong Lou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| | - Li-Hua Zhao
- The Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Kunming 650204, China
| | - Xiao-Jiang Hao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 550002, China
| |
Collapse
|
16
|
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]
|
17
|
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.
Collapse
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
| | | |
Collapse
|
18
|
Paul D, Kundu A, Saha S, Goswami RK. Total synthesis: the structural confirmation of natural products. Chem Commun (Camb) 2021; 57:3307-3322. [DOI: 10.1039/d1cc00241d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This feature article highlights total synthesis as one of the reliable tools for the structural confirmation of natural products.
Collapse
Affiliation(s)
- Debobrata Paul
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Ashis Kundu
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Sanu Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Rajib Kumar Goswami
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| |
Collapse
|
19
|
Zu WY, Tang JW, Hu K, Zhou YF, Gou LL, Su XZ, Lei X, Sun HD, Puno PT. Chaetolactam A, an Azaphilone Derivative from the Endophytic Fungus Chaetomium sp. g1. J Org Chem 2020; 86:475-483. [PMID: 33263391 DOI: 10.1021/acs.joc.0c02214] [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)
- Wen-Yu Zu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
| | - Jian-Wei Tang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
| | - Kun Hu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
| | - Yuan-Fei Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Lei-Lei Gou
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Xiao-Zheng Su
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, Hubei 430074, People’s Republic of China
| | - Han-Dong Sun
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
| | - Pema-Tenzin Puno
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming 650201, Yunnan, People’s Republic of China
| |
Collapse
|
20
|
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]
|
21
|
Assignment of the relative stereochemistry of two novel vicinal dibromo compounds using NMR and DFT-GIAO calculations. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
22
|
Marcarino MO, Zanardi MM, Sarotti AM. The Risks of Automation: A Study on DFT Energy Miscalculations and Its Consequences in NMR-based Structural Elucidation. Org Lett 2020; 22:3561-3565. [DOI: 10.1021/acs.orglett.0c01001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Maribel O. Marcarino
- Instituto de Quı́mica Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, República Argentina
| | - María M. Zanardi
- Facultad de Quı́mica e Ingenierı́a del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Quı́mica Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, República Argentina
| |
Collapse
|
23
|
Howarth A, Ermanis K, Goodman JM. DP4-AI automated NMR data analysis: straight from spectrometer to structure. Chem Sci 2020; 11:4351-4359. [PMID: 34122893 PMCID: PMC8152620 DOI: 10.1039/d0sc00442a] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/02/2020] [Indexed: 01/31/2023] Open
Abstract
A robust system for automatic processing and assignment of raw 13C and 1H NMR data DP4-AI has been developed and integrated into our computational organic molecule structure elucidation workflow. Starting from a molecular structure with undefined stereochemistry or other structural uncertainty, this system allows for completely automated structure elucidation. Methods for NMR peak picking using objective model selection and algorithms for matching the calculated 13C and 1H NMR shifts to peaks in noisy experimental NMR data were developed. DP4-AI achieved a 60-fold increase in processing speed, and near-elimination of the need for scientist time, when rigorously evaluated using a challenging test set of molecules. DP4-AI represents a leap forward in NMR structure elucidation and a step-change in the functionality of DP4. It enables high-throughput analyses of databases and large sets of molecules, which were previously impossible, and paves the way for the discovery of new structural information through machine learning. This new functionality has been coupled with an intuitive GUI and is available as open-source software at https://github.com/KristapsE/DP4-AI.
Collapse
Affiliation(s)
- Alexander Howarth
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Kristaps Ermanis
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jonathan M Goodman
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Armando Navarro-Vázquez
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco, Brazil, 50670-90.1
| |
Collapse
|
25
|
Richardson J, Sharman G, Martínez-Olid F, Cañellas S, Gomez JE. Unlocking the potential of late-stage functionalisation: an accurate and fully automated method for the rapid characterisation of multiple regioisomeric products. REACT CHEM ENG 2020. [DOI: 10.1039/c9re00431a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An automated pipeline for structure determination is outlined that will help unlock the potential of late-stage functionalisation (LSF).
Collapse
Affiliation(s)
| | - Gary Sharman
- Discovery Research and Technologies
- Eli Lilly and Company
- Surrey
- UK
| | - Francisco Martínez-Olid
- Discovery Research and Technologies
- Eli Lilly and Company
- Centro de Investigación Lilly
- 28108 Alcobendas-Madrid
- Spain
| | - Santiago Cañellas
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- E-43007 Tarragona
- Spain
| | - Jose Enrique Gomez
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- E-43007 Tarragona
- Spain
| |
Collapse
|
26
|
Fukaya K, Urabe D, Hiraizumi M, Noguchi K, Matsumoto T, Sakurai K. Computational and Experimental Analysis on the Conformational Preferences of Anticancer Saponin OSW-1. J Org Chem 2019; 85:339-344. [DOI: 10.1021/acs.joc.9b02085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Keisuke Fukaya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Daisuke Urabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Masato Hiraizumi
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Keiichi Noguchi
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Takashi Matsumoto
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
| | - Kaori Sakurai
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| |
Collapse
|
27
|
De Gussem E, Tehrani KA, Herrebout WA, Bultinck P, Johannessen C. Comparative Study of the Vibrational Optical Activity Techniques in Structure Elucidation: The Case of Galantamine. ACS OMEGA 2019; 4:14133-14139. [PMID: 31497733 PMCID: PMC6714543 DOI: 10.1021/acsomega.9b02108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
The absolute configuration of the alkaloid galantamine was studied using a range of solution-state techniques; nuclear magnetic resonance (NMR), vibrational circular dichroism (VCD), and Raman optical activity (ROA). While the combined use of NMR and VCD does provide a fast, high-resolution methodology for determining the absolute configuration of galantamine, both techniques were needed in concert to achieve this goal. ROA, on the other hand, proved to be sensitive enough to assign the full absolute configuration without relying on other techniques. In both cases, statistical validation was applied to aid the determination of absolute configuration. In the case of galantamine, ROA combined with statistical validation is shown to be a powerful stand-alone tool for absolute configuration determination.
Collapse
Affiliation(s)
- Ewoud De Gussem
- Ghent
Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan
281 (S3), 9000 Ghent, Belgium
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | | | - Wouter A. Herrebout
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Patrick Bultinck
- Ghent
Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan
281 (S3), 9000 Ghent, Belgium
| | - Christian Johannessen
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| |
Collapse
|
28
|
Shepherd ED, Dyson BS, Hak WE, Nguyen QNN, Lee M, Kim MJ, Sohn TI, Kim D, Burton JW, Paton RS. Structure Determination of a Chloroenyne from Laurencia majuscula Using Computational Methods and Total Synthesis. J Org Chem 2019; 84:4971-4991. [PMID: 30977652 PMCID: PMC6503471 DOI: 10.1021/acs.joc.8b02975] [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] [Indexed: 01/29/2023]
Abstract
![]()
Despite numerous
advances in spectroscopic methods through the
latter part of the 20th century, the unequivocal structure determination
of natural products can remain challenging, and inevitably, incorrect
structures appear in the literature. Computational methods that allow
the accurate prediction of NMR chemical shifts have emerged as a powerful
addition to the toolbox of methods available for the structure determination
of small organic molecules. Herein, we report the structure determination
of a small, stereochemically rich natural product from Laurencia majuscula using the powerful combination
of computational methods and total synthesis, along with the structure
confirmation of notoryne, using the same approach. Additionally, we
synthesized three further diastereomers of the L. majuscula enyne and have demonstrated that computations are able to distinguish
each of the four synthetic diastereomers from the 32 possible diastereomers
of the natural product. Key to the success of this work is to analyze
the computational data to provide the greatest distinction between
each diastereomer, by identifying chemical shifts that are most sensitive
to changes in relative stereochemistry. The success of the computational
methods in the structure determination of stereochemically rich, flexible
organic molecules will allow all involved in structure determination
to use these methods with confidence.
Collapse
Affiliation(s)
- Erin D Shepherd
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Bryony S Dyson
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - William E Hak
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Quynh Nhu N Nguyen
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Miseon Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 151-742 , Korea
| | - Mi Jung Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 151-742 , Korea
| | - Te-Ik Sohn
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 151-742 , Korea
| | - Deukjoon Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 151-742 , Korea
| | - Jonathan W Burton
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Robert S Paton
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , United Kingdom.,Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| |
Collapse
|
29
|
Immel S, Köck M, Reggelin M. Configurational analysis by residual dipolar couplings: A critical assessment of diastereomeric differentiabilities. Chirality 2019; 31:384-400. [PMID: 30916829 DOI: 10.1002/chir.23065] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 11/06/2022]
Abstract
Two independent statistical models for evaluating the certainties of configurational assignments of compounds based on nuclear magnetic resonance (NMR) data are evaluated and compared. Both methods yield weights or probabilities with which two or more structure models (constitutional or configurational isomers or even conformers) could be differentiated based on experimental parameters. Although this paper focusses on the use of residual dipolar couplings (RDCs) for the differentiation of diastereomers, the concept can be expanded to any set of experimental NMR-derived parameters. It is demonstrated that highly reliable configurational assignments crucially must depend on thorough statistical analysis, which is frequently neglected in the literature.
Collapse
Affiliation(s)
- Stefan Immel
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut (AWI), Helmholtz-Zentrum für Polar- und Meeresforschung, Sektion Ökologische Chemie, Bremerhaven, Germany.,Helmholtz-Zentrum für Infektionsforschung (HZI), Abteilung Chemische Biologie, Braunschweig, Germany
| | - Michael Reggelin
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| |
Collapse
|
30
|
Ermanis K, Parkes KEB, Agback T, Goodman JM. The optimal DFT approach in DP4 NMR structure analysis – pushing the limits of relative configuration elucidation. Org Biomol Chem 2019; 17:5886-5890. [DOI: 10.1039/c9ob00840c] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
What computational methods should be used to achieve the most reliable result in computational structure elucidation? A study on the effect of quality and quantity of geometries on computational NMR structure elucidation performance is reported.
Collapse
Affiliation(s)
- Kristaps Ermanis
- Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | | | - Tatiana Agback
- Medivir AB
- SE-141 22 Huddinge
- Sweden
- Department of Molecular Sciences
- Swedish University of Agricultural Sciences
| | - Jonathan M. Goodman
- Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| |
Collapse
|
31
|
Zhao S, Gensch T, Murray B, Niemeyer ZL, Sigman MS, Biscoe MR. Enantiodivergent Pd-catalyzed C-C bond formation enabled through ligand parameterization. Science 2018; 362:670-674. [PMID: 30237245 PMCID: PMC6613548 DOI: 10.1126/science.aat2299] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/06/2018] [Indexed: 01/01/2023]
Abstract
Despite the enormous potential for the use of stereospecific cross-coupling reactions to rationally manipulate the three-dimensional structure of organic molecules, the factors that control the transfer of stereochemistry in these reactions remain poorly understood. Here we report a mechanistic and synthetic investigation into the use of enantioenriched alkylboron nucleophiles in stereospecific Pd-catalyzed Suzuki cross-coupling reactions. By developing a suite of molecular descriptors of phosphine ligands, we could apply predictive statistical models to select or design distinct ligands that respectively promoted stereoinvertive and stereoretentive cross-coupling reactions. Stereodefined branched structures were thereby accessed through the predictable manipulation of absolute stereochemistry, and a general model for the mechanism of alkylboron transmetallation was proposed.
Collapse
Affiliation(s)
- Shibin Zhao
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Tobias Gensch
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA
| | - Benjamin Murray
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Zachary L Niemeyer
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA.
| | - Mark R Biscoe
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| |
Collapse
|
32
|
Xin D, Jones PJ, Gonnella NC. DiCE: Diastereomeric in Silico Chiral Elucidation, Expanded DP4 Probability Theory Method for Diastereomer and Structural Assignment. J Org Chem 2018; 83:5035-5043. [DOI: 10.1021/acs.joc.8b00338] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dongyue Xin
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, United States
| | - Paul-James Jones
- Information Technology, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, United States
| | - Nina C. Gonnella
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, United States
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Ermanis K, Parkes KEB, Agback T, Goodman JM. Doubling the power of DP4 for computational structure elucidation. Org Biomol Chem 2017; 15:8998-9007. [DOI: 10.1039/c7ob01379e] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Improvements to the DP4 computational structure elucidation method have led to a 2-fold reduction in structural uncertainty and 7-fold improvement of statistical confidence.
Collapse
Affiliation(s)
- K. Ermanis
- Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | | | | | - J. M. Goodman
- Centre for Molecular Science Informatics
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| |
Collapse
|
35
|
Navarro-Vázquez A. State of the art and perspectives in the application of quantum chemical prediction of 1 H and 13 C chemical shifts and scalar couplings for structural elucidation of organic compounds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:29-32. [PMID: 27531665 DOI: 10.1002/mrc.4502] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/13/2016] [Accepted: 08/14/2016] [Indexed: 06/06/2023]
Abstract
Quantum mechanical prediction of chemical shifts and scalar couplings involving 1 H and 13 C nuclei is now a popular tool in structural elucidation of organic compounds. Here, we summarize the current state of the art and present to the reader present limitations and problems, mostly related to treatment of conformational flexibility, as well as future perspectives and potential applications in the field.
Collapse
Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50670-901, Recife, PE, Brazil
| |
Collapse
|