1
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Cuadrado C, Cen-Pacheco F, Daranas AH. Computationally Assisted Analysis of NMR Chemical Shifts as a Tool in Conformational Analysis. Org Lett 2024; 26:6529-6534. [PMID: 38888989 PMCID: PMC11320654 DOI: 10.1021/acs.orglett.4c01642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
A key to understanding the properties of functional molecules is to determine their conformation in solution. A conformational analysis procedure that relies on quantum mechanical calculations and the widely used DP4+ probability was evaluated to decipher the structural information encoded in NMR chemical shifts. The results underscore the potential utility of using NMR chemical shifts in advancing conformational analysis studies of complex molecules in solution.
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Affiliation(s)
- Cristina Cuadrado
- Instituto
de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
| | - Francisco Cen-Pacheco
- Faculty
of Bioanalysis, Iturbide s/n, Veracruz University, 91700 Veracruz, Veracruz, México
| | - Antonio Hernández Daranas
- Instituto
de Productos Naturales y Agrobiología del CSIC (IPNA-CSIC), La Laguna, 38206 Tenerife, Spain
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2
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He JH, Cheng WW, Zhang AQ, Qin SY. Tandem "One-Shot" Measurement of Residual Chemical Shift Anisotropy and Residual Dipolar Coupling using Biphasic Supramolecular Peptide Liquid Crystals. Anal Chem 2024; 96:11881-11889. [PMID: 38976239 DOI: 10.1021/acs.analchem.4c01558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Both solitary and tandem applications of residual chemical shift anisotropy (RCSA) and residual dipolar coupling (RDC) show great potential for the structural and configurational determination of organic molecules. A critical component of both RDC and RCSA methodologies is the alignment medium, whose availability is limited, especially for RCSA measurement. Moreover, reported RDC and RCSA acquisitions mainly rely on two experiments conducted under two different conditions, which are relatively time-consuming and easily cause experimental errors. Herein, a biphasic supramolecular lyotropic liquid crystalline (LLC) system was developed through the self-assembly of C21H43-CONH-V4K3-CONH2, which could act as an alignment medium for not only RDC but also RCSA extraction in DMSO-d6. Notably, the RCSA extraction was easily achieved via one-shot measurement from a single one-dimensional 13C NMR experiment, with no need for special instruments, devices, and correction. Relying on the biphasic LLC medium, meanwhile, RDC data were simply extracted from a single F1-coupled HSQC experiment, different from the standard protocol that requires two spectral acquisitions corresponding to the isotropic and anisotropic conditions. Collectively, the biphasic LLC medium is applicable for tandem RCSA and RDC measurements in one single sample, advancing the stereochemical elucidation of molecules of interest.
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Affiliation(s)
- Jin-Hao He
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Wei-Wei Cheng
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Ai-Qing Zhang
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Si-Yong Qin
- Hubei Engineering Technology Research Centre of Energy Polymer Materials, Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, South-Central Minzu University, Wuhan 430074, P. R. China
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3
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Doro-Goldsmith E, Song Q, Li XL, Li XM, Hu XY, Li HL, Liu HR, Wang BG, Sun H. Absolute Configuration of 12 S-Deoxynortryptoquivaline from Ascidian-Derived Fungus Aspergillus clavatus Determined by Anisotropic NMR and Chiroptical Spectroscopy. JOURNAL OF NATURAL PRODUCTS 2024; 87:381-387. [PMID: 38289330 PMCID: PMC10897928 DOI: 10.1021/acs.jnatprod.3c01157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/24/2024]
Abstract
Tryptoquivalines are highly toxic metabolites initially isolated from the fungus Aspergillus clavatus. The relative and absolute configuration of tryptoquivaline derivates was primarily established by comparison of the chemical shifts, NOE data, and ECD calculations. A de novo determination of the complete relative configuration using NMR spectroscopy was challenging due to multiple spatially separated stereocenters, including one nonprotonated carbon. In this study, we isolated a new tryptoquivaline derivative, 12S-deoxynortryptoquivaline (1), from the marine ascidian-derived fungus Aspergillus clavatus AS-107. The correct assignment of the relative configuration of 1 was accomplished using anisotropic NMR spectroscopy, while the absolute configuration was determined by comparing calculated and experimental ECD spectra. This case study highlights the effectiveness of anisotropic NMR parameters over isotropic NMR parameters in determining the relative configuration of complex natural products without the need for crystallization.
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Affiliation(s)
- Elisa Doro-Goldsmith
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- School
of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Qi Song
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Xiao-Lu Li
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Xiao-Ming Li
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Xue-Yi Hu
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Hong-Lei Li
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
| | - Hao-Ran Liu
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- Institute
of Chemistry, Technische Universität
Berlin, Straße des
17. Juni 135, Berlin 10623, Germany
| | - Bin-Gui Wang
- CAS
and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China
- University
of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Han Sun
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, Berlin 13125, Germany
- Institute
of Chemistry, Technische Universität
Berlin, Straße des
17. Juni 135, Berlin 10623, Germany
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4
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Yu G, Chen Y, Peng Y, Wang G, Zhu M, Zhao X, Yang M, Zhang X, Liu M, He L. Temperature-Controllable Liquid Crystalline Medium for Stereochemical Elucidation of Organic Compounds via Residual Chemical Shift Anisotropies. Anal Chem 2024. [PMID: 38335322 DOI: 10.1021/acs.analchem.3c04477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
The configuration elucidation of organic molecules continues to pose significant challenges in studies involving stereochemistry. Nuclear magnetic resonance (NMR) techniques are powerful for obtaining such structural information. Anisotropic NMR techniques, such as measurement of residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), complementing isotropic NMR parameters, provide relative configuration information. RCSAs provide valuable structural information, especially for nonprotonated carbons, yet have been severely underutilized due to the lack of an easily operational alignment medium capable of rapid transition from anisotropic to isotropic environments, especially in aqueous conditions. In this study, an oligopeptide-based alignment media (FK)4 is presented for RCSA measurements. Temperature variation manipulates the assembly of (FK)4, yielding tunable anisotropic and isotropic phases without the requirement of any special devices or time-consuming correction procedures during data analysis. Decent observed ΔΔRCSA values from sp3 carbons benefit the utilization of RCSA measurements in the structural elucidation of organic molecules highly composed with sp3 carbons. Moreover, the (FK)4 alignment medium is applicable for both RDC and RCSA measurements in one sample, further advancing the configuration analysis of molecules of interest.
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Affiliation(s)
- Gangjin Yu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
| | - Yihao Chen
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Peng
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
| | - Guan Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
| | - Mingjun Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoling Zhao
- Department of Reproductive Medicine General Hospital of Central Theater Command of the People's Liberation Army, Wuhan, Hubei 430061, China
| | - Minghui Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Wuhan,Hubei 430074, China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Fuentes-Monteverde JC, Noll M, Das A, Immel S, Reggelin M, Griesinger C, Nath N. Residual-Chemical-Shift-Anisotropy-Based Enantiodifferentiation in Lyotropic Liquid Crystalline Phases Based on Helically Chiral Polyacetylenes. Angew Chem Int Ed Engl 2023; 62:e202309981. [PMID: 37684219 DOI: 10.1002/anie.202309981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/10/2023]
Abstract
Anisotropic NMR spectroscopy, revealing residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) has emerged as a powerful tool to determine the configurations of synthetic and complex natural compounds. The deduction of the absolute in addition to the relative configuration is one of the primary goals in the field. Therefore, the investigation of the enantiodiscriminating capabilities of chiral alignment media becomes essential. While RDCs and RCSAs are now used for the determination of the relative configuration routinely, RCSAs have not been measured in chiral alignment media such as chiral liquid crystals. Herein, we present this application by measuring RCSAs for chiral analytes such as indanol and isopinocampheol in the lyotropic liquid crystalline phase of an L-valine derived helically chiral polyacetylenes. We have also demonstrated that a single 1D 13 C-{1 H} NMR spectrum suffices to get the RCSAs circumventing the necessity to acquire two spectra at two alignment conditions.
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Affiliation(s)
- Juan Carlos Fuentes-Monteverde
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-Based Structural Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Noll
- Department of Chemistry, Technical University of Darmstadt, Alarich Weiss Straße 4, 64287, Darmstadt, Germany
| | - Akhi Das
- Department of Chemistry, Gauhati University Guwahati, Jalukbari, 781014, India
| | - Stefan Immel
- Department of Chemistry, Technical University of Darmstadt, Alarich Weiss Straße 4, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Department of Chemistry, Technical University of Darmstadt, Alarich Weiss Straße 4, 64287, Darmstadt, Germany
| | - Christian Griesinger
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-Based Structural Biology, Am Fassberg 11, 37077, Göttingen, Germany
| | - Nilamoni Nath
- Department of Chemistry, Gauhati University Guwahati, Jalukbari, 781014, India
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6
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Silva Elipe MV, Ndukwe IE, Navarro-Vázquez A. Anisotropic NMR data acquisition with a prototype 400 MHz cryogen-free NMR spectrometer. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:530-543. [PMID: 37530063 DOI: 10.1002/mrc.5380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
High-temperature superconducting (HTS) materials have recently been incorporated into the construction of HTS cryogen-free magnets for nuclear magnetic resonance (NMR) spectroscopy. These HTS NMR spectrometers do not require liquid cryogens, thereby providing significant cost savings and facilitating easy integration into chemistry laboratories. However, the optimal performance of these HTS magnets against standard cryogen NMR magnets must be evaluated, especially with demanding modern NMR applications such as NMR in anisotropic media. The stability of the HTS magnets over time and their performance with complex pulse sequence experiments are the main unknown factors of this new technology. In this study, we evaluate the utility of our prototype 400 MHz cryogen-free power-driven HTS NMR spectrometer, installed in the fumehood of a chemistry laboratory, for stereochemical analysis of three commercial natural products (artemisinin, artemether, and dihydroartemisinin) via measurement of anisotropic NMR data, in particular, residual dipolar couplings. The accuracy of measurement of the anisotropic NMR data with the HTS magnet spectrometer is evaluated through the CASE-3D fitting protocol, as implemented in the Mestrenova-StereoFitter software program.
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Affiliation(s)
| | | | - Armando Navarro-Vázquez
- Departmento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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7
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Hirschmann M, Soltwedel O, Ritzert P, von Klitzing R, Thiele CM. Light-Controlled Lyotropic Liquid Crystallinity of Polyaspartates Exploited as Photo-Switchable Alignment Medium. J Am Chem Soc 2023; 145:3615-3623. [PMID: 36749116 DOI: 10.1021/jacs.2c12760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Two polyaspartates bearing ortho-fluorinated azobenzenes (pFAB) as photo-responsive groups in the side chain were synthesized: PpFABLA (1) and co-polyaspartate PpFABLA-co-PBLA [11, 75%(n/n) PpFABLA content]. As a consequence of the E/Z-isomerization of the side chain, PpFABLA (1) undergoes a visible-light-induced reversible coil-helix transition in solution: Green light (525 nm) affords the coil, and violet light (400 nm) affords the helix. pFAB significantly increases the thermal stability of the Z-isomer at 20 °C (t1/2 = 66 d for the Z-isomer) and effectively counters the favored back formation of the helix. At 20%(w/w) polymer concentration, the helical polymer forms a lyotropic liquid crystal (LLC) that further orients unidirectionally inside a magnetic field, while the coil polymer results in an isotropic solution. The high viscosity of the polymer solution stabilizes the coexistence of liquid crystalline and isotropic domains, which were obtained with spatial control by partial light irradiation. When used as an alignment medium, PpFABLA (1) enables (i) the measurement of dipolar couplings without the need for a separate isotropic reference and (ii) the differentiation of enantiomers. PpFABLA-co-PBLA (11) preserves the helical structure, by intention, independently of the E/Z-isomerization of the side chain: Both photo-isomers of PpFABLA-co-PBLA (11) form a helix that─at a concentration of 16%(w/w)─form an LLC. Despite the absence of a change in the secondary structure, the E/Z-isomerization of the side chain changes the morphology of the liquid crystal and leads to different sets of dipolar coupling for the same probe molecule.
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Affiliation(s)
- Max Hirschmann
- Clemens-Schöpf-Institute, Technical University of Darmstadt (TUDa), Alarich-Weiss-Straße 4, DE 64287 Darmstadt, Germany
| | - Olaf Soltwedel
- Institute for Condensed Matter Physics, Technical University of Darmstadt (TUDa), Hochschulstraße 8, DE 64289 Darmstadt, Germany
| | - Philipp Ritzert
- Institute for Condensed Matter Physics, Technical University of Darmstadt (TUDa), Hochschulstraße 8, DE 64289 Darmstadt, Germany
| | - Regine von Klitzing
- Institute for Condensed Matter Physics, Technical University of Darmstadt (TUDa), Hochschulstraße 8, DE 64289 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institute, Technical University of Darmstadt (TUDa), Alarich-Weiss-Straße 4, DE 64287 Darmstadt, Germany
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8
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Carvalho DS, da Silva DGB, Hallwass F, Navarro-Vázquez A. An Acrylonitrile-Based Copolymer Gel as an NMR Alignment Medium for Extraction of Residual Dipolar Couplings of Small Molecules in Aqueous Solution. Chempluschem 2023; 88:e202200446. [PMID: 36782376 DOI: 10.1002/cplu.202200446] [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: 12/12/2022] [Revised: 01/19/2023] [Indexed: 01/24/2023]
Abstract
An NMR weakly-aligning polymer gel has been prepared by copolymerization of acrylonitrile and 2-acrylamide-2-methyl-1-propanesulfonic acid in the presence of 1,4-butanediol diacrylate as a cross-linker. The polymer readily swells in water in a large range of temperatures, although the swelling ratio is decreased in saline solutions. The swollen gel can be mechanically compressed, in a reversible way, generating anisotropy, as easily shown in 2 H NMR experiments, and allowing measurement of 1 DCH residual dipolar couplings (RDCs) through F1-coupled HSQC experiments. The performance of this gel as a NMR alignment medium was evaluated in several water-soluble organic molecules and, while it provided RDCs of proper size for sucrose and even such as small molecule as 5-norbornen-2-ol, in the case of azidothymidine and cefuroxime sodium salt the strong interaction of these molecules with the gel prevented successful extraction of the RDCs.
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Affiliation(s)
- Daiane S Carvalho
- Departamento de Química Fundamental, Universidade Federal de Pernambuco Cidade Universitria, CEP, 50.740-540, Recife, PE, Brazil
| | - Danilo G B da Silva
- Departamento de Química Fundamental, Universidade Federal de Pernambuco Cidade Universitria, CEP, 50.740-540, Recife, PE, Brazil
| | - Fernando Hallwass
- Departamento de Química Fundamental, Universidade Federal de Pernambuco Cidade Universitria, CEP, 50.740-540, Recife, PE, Brazil
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco Cidade Universitria, CEP, 50.740-540, Recife, PE, Brazil
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9
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Stereochemical investigation of flexible macrocyclic cembranes depending on residual dipolar couplings method. Tetrahedron 2023. [DOI: 10.1016/j.tet.2023.133301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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10
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Liu Y, Ndukwe IE, Reibarkh M, Martin GE, Williamson RT. Prediction of anisotropic NMR data without knowledge of alignment medium structure by surface decomposition. Phys Chem Chem Phys 2022; 24:20164-20182. [PMID: 35996986 DOI: 10.1039/d2cp02621j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prediction of anisotropic NMR data directly from solute-medium interaction is of significant theoretical and practical interest, particularly for structure elucidation, configurational analysis and conformational studies of complex organic molecules and natural products. Current prediction methods require an explicit structural model of the alignment medium: a requirement either impossible or impractical on a scale necessary for small organic molecules. Here we formulate a comprehensive mathematical framework for a parametrization protocol that deconvolutes an arbitrary surface of the medium into several simple local landscapes that are distributed over the medium's surface by specific orientational order parameters. The shapes and order parameters of these local landscapes are determined via fitting that maximizes the congruence between experimentally determined anisotropic NMR measurables and their predicted counterparts, thus avoiding the need for an a priori knowledge of the global medium morphology. This method achieves substantial improvements in the accuracy of predicted anisotropic NMR values compared to current methods, as demonstrated herein with sixteen natural products. Furthermore, because this formalism extracts structural commonalities of the medium by combining anisotropic NMR data from different compounds, its robustness and accuracy are expected to improve as more experimental data become available for further re-optimization of fitting parameters.
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Affiliation(s)
- Yizhou Liu
- Analytical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT, 06340, USA.
| | - Ikenna E Ndukwe
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Gary E Martin
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - R Thomas Williamson
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
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11
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Fuentes-Monteverde JCC, Nath N, Forero AM, Balboa EM, Navarro-Vázquez A, Griesinger C, Jiménez C, Rodríguez J. Connection of Isolated Stereoclusters by Combining 13C-RCSA, RDC, and J-Based Configurational Analyses and Structural Revision of a Tetraprenyltoluquinol Chromane Meroterpenoid from Sargassum muticum. Mar Drugs 2022; 20:462. [PMID: 35877755 PMCID: PMC9319238 DOI: 10.3390/md20070462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/06/2022] [Accepted: 07/15/2022] [Indexed: 12/10/2022] Open
Abstract
The seaweed Sargassum muticum, collected on the southern coast of Galicia, yielded a tetraprenyltoluquinol chromane meroditerpene compound known as 1b, whose structure is revised. The relative configuration of 1b was determined by J-based configurational methodology combined with an iJ/DP4 statistical analysis and further confirmed by measuring two anisotropic properties: carbon residual chemical shift anisotropies (13C-RCSAs) and one-bond 1H-13C residual dipolar couplings (1DCH-RDCs). The absolute configuration of 1b was deduced by ECD/OR/TD-DFT methods and established as 3R,7S,11R.
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Affiliation(s)
- Juan Carlos C. Fuentes-Monteverde
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
- NMR Based Structural Biology, MPI for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Nilamoni Nath
- Department of Chemistry, Gauhati University, Gopinath Bardoloi Nagar, Guwahati 781014, India;
| | - Abel M. Forero
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
| | - Elena M. Balboa
- Department of Chemical Engineering, Faculty of Science, Campus Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain;
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Cidade Universitária, Recife 50740-550, Brazil;
| | - Christian Griesinger
- NMR Based Structural Biology, MPI for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carlos Jiménez
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
| | - Jaime Rodríguez
- Departamento de Química e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain; (J.C.C.F.-M.); (A.M.F.)
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12
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Yu G, Wang G, Duan M, Jiang B, Zhang X, Li C, He L, Liu M. Self-Assembled Oligopeptide (FK) 4 as a Chiral Alignment Medium for the Anisotropic NMR Analysis of Organic Compounds. ACS APPLIED MATERIALS & INTERFACES 2022; 14:29223-29229. [PMID: 35712808 DOI: 10.1021/acsami.2c05506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anisotropic NMR parameters have been proven to be powerful for the structural elucidation of organic molecules. Herein, we present an alignment medium based on the self-assembled (FK)4 oligopeptide, showing excellent properties in measurements of anisotropic NMR parameters in both D2O and CD3OD. The preparation of the (FK)4-based alignment medium is simple and rapid. The low viscosity of the anisotropic phase makes it easy to be transferred to the NMR tube. The alignment of the oligopeptide is fast, stable, and homogeneous, with weak background signals, permitting the acquirement of high-quality NMR spectra. The performance of this alignment medium in residual dipolar coupling measurements and diastereomer discriminations is demonstrated by analyzing several different analytes. The enantiodiscrimination property of the (FK)4 oligopeptide is revealed by the difference of residual chemical shift anisotropy of the two enantiomers in the 1D 13C spectrum, granting its potential use for the quantification and identification of enantiomers of small molecules.
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Affiliation(s)
- Gangjin Yu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guan Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mojie Duan
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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13
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Berdagué P, Gouilleux B, Noll M, Immel S, Reggelin M, Lesot P. Study and quantification of enantiodiscrimination power of four polymeric chiral LLCs using NAD 2D-NMR. Phys Chem Chem Phys 2022; 24:7338-7348. [DOI: 10.1039/d1cp04915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identifying and understanding the role of key molecular factors involved in the orientation/discrimination phenomena of analytes in polymer-based chiral liquid crystals (CLCs) are essential tasks for optimizing computational predictions (molecular...
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14
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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.
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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
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15
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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16
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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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17
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Burns DC, Reynolds WF. Minimizing the risk of deducing wrong natural product structures from NMR data. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:500-533. [PMID: 33855734 DOI: 10.1002/mrc.4933] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 06/12/2023]
Abstract
There continues to be a disturbing number of natural products reported in the literature whose structures are incorrect. At least in part, this reflects the fact that many natural product chemists have limited formal nuclear magnetic resonance training. Gaps in training and lack of awareness regarding the challenges and ambiguities associated with two-dimensional nuclear magnetic resonance data interpretation can easily lead to errors in structure elucidation. The purpose of this tutorial is to point out some of these issues, highlight the kinds of errors that have been made and provide specific advice on how to avoid these missteps such that the risk of reporting a wrong structure is minimized.
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Affiliation(s)
- Darcy C Burns
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - William F Reynolds
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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18
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de Melo Sousa CM, Giordani RB, de Almeida WAM, Griesinger C, Gil RR, Navarro-Vázquez A, Hallwass F. Effect of the solvent on the conformation of monocrotaline as determined by isotropic and anisotropic NMR parameters. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:561-568. [PMID: 31715029 DOI: 10.1002/mrc.4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
The conformation in solution of monocrotaline, a pyrrolizidine alkaloid presenting an eleven-membered macrocyclic diester ring, has been investigated using a combination of isotropic and anisotropic nuclear magnetic resonance parameters measured in four solvents of different polarity (D2 O, DMSO-d6 , CDCl3 , and C6 D6 ). Anisotropic nuclear magnetic resonance parameters were measured in different alignment media, based on their compatibility with the solvent of interest: cromoglycate liquid crystal solution was used for D2 O, whereas a poly (methyl methacrylate) polymer gel was chosen for CDCl3 and C6 D6 , and a poly (hydroxyethyl methacrylate) gel for DMSO-d6 . Whereas the pyrrolizidine ring shows an E6 exo-puckered conformation in all of the solvents, the macrocyclic eleven-membered ring adopts different populations of syn-parallel and anti-parallel relative orientation of the carbonyl groups according to the polarity of the solvent.
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Affiliation(s)
- Cleyton Marcos de Melo Sousa
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
- Instituto Federal de Pernambuco, Caruaru, Pernambuco, Brazil
| | - Raquel Brandt Giordani
- Laboratório de Farmacognosia, Departamento de Farmácia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Christian Griesinger
- Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Fernando Hallwass
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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19
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Das A, Nath N. Elucidating natural product structures using a robust measurement of carbon residual chemical shift anisotropy combined with DFT. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:569-576. [PMID: 31758720 DOI: 10.1002/mrc.4975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/20/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
Determination of configurations and conformations is an important step in the structural characterization of small molecules. Apart from utilizing isotropic J-couplings and nuclear overhauser effect (NOEs) measured in isotropic solution, anisotropic Nuclear Magnetic resonance (NMR) data such as residual dipolar couplings and residual chemical shift anisotropies (RCSAs) were also used to elucidate complex small molecule structures. Measuring RCSA has always been historically difficult due to the isotropic shift effect accompanied by molecular alignment and therefore only occasionally applied in a few examples. Here, we present a robust measurement of carbon RCSAs using a smaller gel-stretching device to determine the structures of a few small molecules. A systematic study on how different density functional theory computed anisotropies of the chemical shift anisotropy tensors impact RCSA data interpretation has also been discussed. We also discuss the effect of utilizing various carbons as reference nuclei for RCSA data extraction as well as the orientation behavior of estrone in orthogonal alignment media.
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Affiliation(s)
- Akhi Das
- Department of Chemistry, Gauhati University, Guwahati, India
| | - Nilamoni Nath
- Department of Chemistry, Gauhati University, Guwahati, India
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20
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da Silva DGB, Hallwass F, Navarro-Vázquez A. Single experiment measurement of residual dipolar couplings in aqueous solution using a biphasic bisperylene imide chromonic liquid crystal. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:408-413. [PMID: 33295034 DOI: 10.1002/mrc.5120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/01/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
The use of the biphasic isotropic/nematic region in a bisperylene imide-based lyotropic liquid crystal system allows the extraction of proton-carbon 1 DCH residual dipolar couplings in aqueous solution from a single F1-coupled HSQC experiment. The method was successfully applied to the RDC-based conformational analysis of sucrose.
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Affiliation(s)
- Danilo G B da Silva
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Fernando Hallwass
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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21
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Porras G, Chassagne F, Lyles JT, Marquez L, Dettweiler M, Salam AM, Samarakoon T, Shabih S, Farrokhi DR, Quave CL. Ethnobotany and the Role of Plant Natural Products in Antibiotic Drug Discovery. Chem Rev 2021; 121:3495-3560. [PMID: 33164487 PMCID: PMC8183567 DOI: 10.1021/acs.chemrev.0c00922] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The crisis of antibiotic resistance necessitates creative and innovative approaches, from chemical identification and analysis to the assessment of bioactivity. Plant natural products (NPs) represent a promising source of antibacterial lead compounds that could help fill the drug discovery pipeline in response to the growing antibiotic resistance crisis. The major strength of plant NPs lies in their rich and unique chemodiversity, their worldwide distribution and ease of access, their various antibacterial modes of action, and the proven clinical effectiveness of plant extracts from which they are isolated. While many studies have tried to summarize NPs with antibacterial activities, a comprehensive review with rigorous selection criteria has never been performed. In this work, the literature from 2012 to 2019 was systematically reviewed to highlight plant-derived compounds with antibacterial activity by focusing on their growth inhibitory activity. A total of 459 compounds are included in this Review, of which 50.8% are phenolic derivatives, 26.6% are terpenoids, 5.7% are alkaloids, and 17% are classified as other metabolites. A selection of 183 compounds is further discussed regarding their antibacterial activity, biosynthesis, structure-activity relationship, mechanism of action, and potential as antibiotics. Emerging trends in the field of antibacterial drug discovery from plants are also discussed. This Review brings to the forefront key findings on the antibacterial potential of plant NPs for consideration in future antibiotic discovery and development efforts.
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Affiliation(s)
- Gina Porras
- Center for the Study of Human Health, Emory University, 1557 Dickey Dr., Atlanta, Georgia 30322
| | - François Chassagne
- Center for the Study of Human Health, Emory University, 1557 Dickey Dr., Atlanta, Georgia 30322
| | - James T. Lyles
- Center for the Study of Human Health, Emory University, 1557 Dickey Dr., Atlanta, Georgia 30322
| | - Lewis Marquez
- Molecular and Systems Pharmacology Program, Laney Graduate School, Emory University, 615 Michael St., Whitehead 115, Atlanta, Georgia 30322
| | - Micah Dettweiler
- Department of Dermatology, Emory University, 615 Michael St., Whitehead 105L, Atlanta, Georgia 30322
| | - Akram M. Salam
- Molecular and Systems Pharmacology Program, Laney Graduate School, Emory University, 615 Michael St., Whitehead 115, Atlanta, Georgia 30322
| | - Tharanga Samarakoon
- Emory University Herbarium, Emory University, 1462 Clifton Rd NE, Room 102, Atlanta, Georgia 30322
| | - Sarah Shabih
- Center for the Study of Human Health, Emory University, 1557 Dickey Dr., Atlanta, Georgia 30322
| | - Darya Raschid Farrokhi
- Center for the Study of Human Health, Emory University, 1557 Dickey Dr., Atlanta, Georgia 30322
| | - Cassandra L. Quave
- Center for the Study of Human Health, Emory University, 1557 Dickey Dr., Atlanta, Georgia 30322
- Emory University Herbarium, Emory University, 1462 Clifton Rd NE, Room 102, Atlanta, Georgia 30322
- Department of Dermatology, Emory University, 615 Michael St., Whitehead 105L, Atlanta, Georgia 30322
- Molecular and Systems Pharmacology Program, Laney Graduate School, Emory University, 615 Michael St., Whitehead 115, Atlanta, Georgia 30322
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22
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Monroe AZ, Gordon WH, Wood JS, Martin GE, Morgan JB, Williamson RT. Structural revision of a Wnt/β-catenin modulator and confirmation of cannabielsoin constitution and configuration. Chem Commun (Camb) 2021; 57:5658-5661. [DOI: 10.1039/d1cc01971f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this report, we revise the structure for a previously reported synthetic product proposed to be the 1R,2S-cannabidiol epoxide and reassign it as cannabielsoin using anisotropic NMR and synthetic chemistry methods.
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Affiliation(s)
- Angelina Z. Monroe
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - William H. Gordon
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - Jared S. Wood
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - Gary E. Martin
- Department of Chemistry
- Seton Hall University
- South Orange
- USA
| | - Jeremy B. Morgan
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
| | - R. Thomas Williamson
- Department of Chemistry & Biochemistry
- University of North Carolina Wilmington
- Wilmington
- USA
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23
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Recchia MJJ, Cohen RD, Liu Y, Sherer EC, Harper JK, Martin GE, Williamson RT. "One-Shot" Measurement of Residual Chemical Shift Anisotropy Using Poly-γ-benzyl-l-glutamate as an Alignment Medium. Org Lett 2020; 22:8850-8854. [PMID: 33140974 DOI: 10.1021/acs.orglett.0c03225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A method for the measurement of residual chemical shift anisotropy in one experiment using a biphasic isotropic/anisotropic lyotropic liquid crystalline medium based on poly-γ-benzyl-l-glutamate as the alignment medium is presented. This approach is demonstrated on the model compound strychnine and neotricone, a depsidone natural product with a questionable structural assignment based on comparison with the closely related excelsione and in-depth density functional theory calculations.
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Affiliation(s)
- Michael J J Recchia
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Ryan D Cohen
- Analytical Research & Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - Yizhou Liu
- Analytical Research & Development, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Edward C Sherer
- Analytical Research & Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Gary E Martin
- Department of Chemistry, Seton Hall University, South Orange, New Jersey 07079, United States
| | - R Thomas Williamson
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
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24
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Structure elucidation of small organic molecules by contemporary computational chemistry methods. Arch Pharm Res 2020; 43:1114-1127. [DOI: 10.1007/s12272-020-01277-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
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25
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Lesot P, Gil RR, Berdagué P, Navarro-Vázquez A. Deuterium Residual Quadrupolar Couplings: Crossing the Current Frontiers in the Relative Configuration Analysis of Natural Products. JOURNAL OF NATURAL PRODUCTS 2020; 83:3141-3148. [PMID: 32970418 DOI: 10.1021/acs.jnatprod.0c00745] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The determination of the 3D structure (configuration and preferred conformation) of complex natural and synthetic organic molecules is a long-standing but still challenging task for chemists, with various implications in pharmaceutical sciences whether or not these substances have specific bioactivities. Nuclear magnetic resonance (NMR) in aligning media, either lyotropic liquid crystals (LLCs) or polymer gels, in combination with molecular modeling is a unique framework for solving complex structural problems whose analytical wealth lies in the establishment of nonlocal structural correlations. As an alternative to the already well-established anisotropic NMR parameters, such as RDCs (residual dipolar couplings) and RCSAs (residual chemical shift anisotropies), it is shown here that deuterium residual quadrupolar couplings (2H-RQCs) can be extracted from 2H 2D-NMR spectra recorded at the natural abundance level in samples oriented in a homopolypeptide LLCs (poly-γ-benzyl-l-glutamate (PBLG)). These 2H-RQCs were successfully used to address nontrivial structural problems in organic molecules. The performance and scope of this new tool is examined for two natural chiral compounds of pharmaceutical interest (strychnine and artemisinin). This is the first report in which the 3D structure/relative configuration of complex bioactive molecules is unambiguously determined using only 2H-RQCs, which, in this case, are at 2H natural abundance.
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Affiliation(s)
- Philippe Lesot
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15 rue du Doyen, Georges Poitou, F-91405 Orsay, France
- Centre National de la Recherche Scientifique (CNRS), 3 rue Michel Ange, F-75016 Paris, France
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Philippe Berdagué
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15 rue du Doyen, Georges Poitou, F-91405 Orsay, France
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, CEP 50.740-540 Recife, Pernambuco, Brazil
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26
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Ndukwe IE, Lam YH, Pandey SK, Haug BE, Bayer A, Sherer EC, Blinov KA, Williamson RT, Isaksson J, Reibarkh M, Liu Y, Martin GE. Unequivocal structure confirmation of a breitfussin analog by anisotropic NMR measurements. Chem Sci 2020; 11:12081-12088. [PMID: 34094423 PMCID: PMC8162999 DOI: 10.1039/d0sc03664a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Structural features of proton-deficient heteroaromatic natural products, such as the breitfussins, can severely complicate their characterization by NMR spectroscopy. For the breitfussins in particular, the constitution of the five-membered oxazole central ring cannot be unequivocally established via conventional NMR methods when the 4′-position is halogenated. The level of difficulty is exacerbated by 4′-iodination, as the accuracy with which theoretical NMR parameters are determined relies extensively on computational treatment of the relativistic effects of the iodine atom. It is demonstrated in the present study, that the structure of a 4′-iodo breitfussin analog can be unequivocally established by anisotropic NMR methods, by adopting a reduced singular value decomposition (SVD) protocol that leverages the planar structures exhibited by its conformers. Structural features of proton-deficient heteroaromatic natural products, such as the breitfussins, can severely complicate their characterization by NMR spectroscopy.![]()
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Affiliation(s)
- Ikenna E Ndukwe
- Analytical Research & Development, (Rahway), Merck & Co. Inc. Kenilworth NJ USA
| | - Yu-Hong Lam
- Computational and Structural Chemistry, Merck & Co., Inc. Rahway NJ 07065 USA
| | - Sunil K Pandey
- Department of Chemistry and Centre for Pharmacy, University of Bergen Allégaten 41 NO-5020 Bergen Norway
| | - Bengt E Haug
- Department of Chemistry and Centre for Pharmacy, University of Bergen Allégaten 41 NO-5020 Bergen Norway
| | - Annette Bayer
- Department of Chemistry, UiT the Arctic University of Tromsø NO-9037 Tromsø Norway
| | - Edward C Sherer
- Analytical Research & Development, (Rahway), Merck & Co. Inc. Kenilworth NJ USA
| | - Kirill A Blinov
- MestReLab Research S. L. Santiago de Compostela A Coruna 15706 Spain
| | - R Thomas Williamson
- Analytical Research & Development, (Rahway), Merck & Co. Inc. Kenilworth NJ USA
| | - Johan Isaksson
- Department of Chemistry, UiT the Arctic University of Tromsø NO-9037 Tromsø Norway
| | - Mikhail Reibarkh
- Analytical Research & Development, (Rahway), Merck & Co. Inc. Kenilworth NJ USA
| | - Yizhou Liu
- Analytical Research & Development, (Rahway), Merck & Co. Inc. Kenilworth NJ USA
| | - Gary E Martin
- Analytical Research & Development, (Rahway), Merck & Co. Inc. Kenilworth NJ USA
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27
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Qin S, Jiang Y, Sun H, Liu H, Zhang A, Lei X. Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid‐Crystalline‐Based Medium. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Si‐Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Yan Jiang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Han Sun
- Section of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) 13125 Berlin Germany
| | - Han Liu
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ai‐Qing Zhang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Xinxiang Lei
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
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28
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Relative configuration of micrograms of natural compounds using proton residual chemical shift anisotropy. Nat Commun 2020; 11:4372. [PMID: 32873801 PMCID: PMC7463026 DOI: 10.1038/s41467-020-18093-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 07/28/2020] [Indexed: 01/12/2023] Open
Abstract
3D molecular structure determination is a challenge for organic compounds or natural products available in minute amounts. Proton/proton and proton/carbon correlations yield the constitution. J couplings and NOEs oftentimes supported by one-bond 1H,13C residual dipolar couplings (RDCs) or by 13C residual chemical shift anisotropies (RCSAs) provide the relative configuration. However, these RDCs or carbon RCSAs rely on 1% natural abundance of 13C preventing their use for compounds available only in quantities of a few 10’s of µgs. By contrast, 1H RCSAs provide similar information on spatial orientation of structural moieties within a molecule, while using the abundant 1H spin. Herein, 1H RCSAs are accurately measured using constrained aligning gels or liquid crystals and applied to the 3D structural determination of molecules with varying complexities. Even more, deuterated alignment media allow the elucidation of the relative configuration of around 35 µg of a briarane compound isolated from Briareum asbestinum. Determination of 3D molecular structures remains challenging for natural products or organic compounds available in minute amounts. Here, the authors determine the structure of complex molecules, including few micrograms of briarane B-3 isolated from Briareum asbestinums, through measurement of 1H residual chemical shift anisotropy.
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29
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Qin S, Jiang Y, Sun H, Liu H, Zhang A, Lei X. Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid‐Crystalline‐Based Medium. Angew Chem Int Ed Engl 2020; 59:17097-17103. [DOI: 10.1002/anie.202007243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Si‐Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Yan Jiang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Han Sun
- Section of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) 13125 Berlin Germany
| | - Han Liu
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ai‐Qing Zhang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Xinxiang Lei
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
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30
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Ndukwe IE, Wang X, Lam NYS, Ermanis K, Alexander KL, Bertin MJ, Martin GE, Muir G, Paterson I, Britton R, Goodman JM, Helfrich EJN, Piel J, Gerwick WH, Williamson RT. Synergism of anisotropic and computational NMR methods reveals the likely configuration of phormidolide A. Chem Commun (Camb) 2020; 56:7565-7568. [PMID: 32520016 PMCID: PMC7436192 DOI: 10.1039/d0cc03055d] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Characterization of the complex molecular scaffold of the marine polyketide natural product phormidolide A represents a challenge that has persisted for nearly two decades. In light of discordant results arising from recent synthetic and biosynthetic reports, a rigorous study of the configuration of phormidolide A was necessary. This report outlines a synergistic effort employing computational and anisotropic NMR investigation, that provided orthogonal confirmation of the reassigned side chain, as well as supporting a further correction of the C7 stereocenter.
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Affiliation(s)
- Ikenna E Ndukwe
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Xiao Wang
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, USA
| | - Nelson Y S Lam
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kristaps Ermanis
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kelsey L Alexander
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA and Department of Chemistry, University of California, San Diego, CA, USA
| | - Matthew J Bertin
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
| | - Gary E Martin
- Department of Chemistry, Seton Hall University, South Orange, NJ, USA
| | - Garrett Muir
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Ian Paterson
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | | | - Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - William H Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - R Thomas Williamson
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, NC, USA.
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31
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Virgili A, Granados A, Jaime C, Suárez-López R, Parella T, Monteagudo E. Evidence of Enantiomers of Spiroglycol. Distinction by Using α,α′-Bis(trifluoromethyl)-9,10-anthracenedimethanol as a Chiral Solvating Agent and by Derivatization with Chiral Acids. J Org Chem 2020; 85:7247-7257. [DOI: 10.1021/acs.joc.0c00578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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32
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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
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33
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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Determination of Complex Small-Molecule Structures Using Molecular Alignment Simulation. Angew Chem Int Ed Engl 2020; 59:6172-6176. [PMID: 31971323 PMCID: PMC7187346 DOI: 10.1002/anie.202000311] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/23/2020] [Indexed: 11/12/2022]
Abstract
Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy-based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule-specific anisotropic NMR parameters. The quantitative correlation uses an accurate three-dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ-benzyl-l-glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.
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Affiliation(s)
- Alain Ibáñez de Opakua
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
| | - Frederik Klama
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGA30602USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry and BiochemistrySeton Hall UniversitySouth OrangeNJ07079USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry & BiochemistryUniversity of North Carolina WilmingtonWilmingtonNC28409USA
| | - Markus Zweckstetter
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
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34
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Koos MRM, Navarro‐Vázquez A, Anklin C, Gil RR. Computer‐Assisted 3D Structure Elucidation (CASE‐3D): The Structural Value of
2
J
CH
in Addition to
3
J
CH
Coupling Constants. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
| | | | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
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35
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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Bestimmung komplexer kleiner Molekülstrukturen mittels molekularer Ausrichtungssimulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alain Ibáñez de Opakua
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
| | - Frederik Klama
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Complex Carbohydrate Research CenterUniversity of Georgia Athens GA 30602 USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry and BiochemistrySeton Hall University South Orange NJ 07079 USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry & BiochemistryUniversity of North Carolina Wilmington Wilmington NC 28409 USA
| | - Markus Zweckstetter
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
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36
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Li XL, Chi LP, Navarro-Vázquez A, Hwang S, Schmieder P, Li XM, Li X, Yang SQ, Lei X, Wang BG, Sun H. Stereochemical Elucidation of Natural Products from Residual Chemical Shift Anisotropies in a Liquid Crystalline Phase. J Am Chem Soc 2020; 142:2301-2309. [PMID: 31889437 DOI: 10.1021/jacs.9b10961] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Determination of the stereochemistry of organic molecules still represents one of the major obstacles in the structure elucidation procedure in drug discovery. Although the application of residual dipolar couplings (RDCs) has revolutionized this field, residual chemical shift anisotropies (RCSAs) which contain valuable structural information for nonprotonated carbons have only been scarcely employed so far. In this study, we present a simple but highly effective solution to extract RCSAs of the analytes in a liquid crystalline phase formed by AAKLVFF oligopeptides. This method does not require any special instruments, devices, or correction during postacquisition data analysis and thus can be easily applied in any chemistry laboratory. To illustrate the potential of this method, the relative configurations of four known natural products (1-4) belonging to different structural classes were confirmed. Moreover, we unambiguously elucidated the stereochemistry of spiroepicoccin A (5), a rare thiodiketopiperazine marine natural product whose configuration could not be assigned based on conventional NMR methods.
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Affiliation(s)
- Xiao-Lu Li
- Section of Structural Biology , Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Berlin 13125 , Germany
| | - Lu-Ping Chi
- Laboratory of Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266071 , People's Republic of China.,University of Chinese Academy of Sciences , Yuquan Road 19A , Beijing 100049 , People's Republic of China
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental , Universidade Federal de Pernambuco , Recife , Pernambuco 50670-901 , Brazil
| | - Songhwan Hwang
- Section of Structural Biology , Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Berlin 13125 , Germany
| | - Peter Schmieder
- Section of Structural Biology , Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Berlin 13125 , Germany
| | - Xiao-Ming Li
- Laboratory of Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266071 , People's Republic of China
| | - Xin Li
- Laboratory of Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266071 , People's Republic of China
| | - Sui-Qun Yang
- Laboratory of Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266071 , People's Republic of China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences , South Central University for Nationalities , Wuhan 430074 , People's Republic of China
| | - Bin-Gui Wang
- Laboratory of Marine Biology and Biotechnology , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266071 , People's Republic of China
| | - Han Sun
- Section of Structural Biology , Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Berlin 13125 , Germany
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37
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Lesot P, Aroulanda C, Berdagué P, Meddour A, Merlet D, Farjon J, Giraud N, Lafon O. Multinuclear NMR in polypeptide liquid crystals: Three fertile decades of methodological developments and analytical challenges. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:85-154. [PMID: 32130960 DOI: 10.1016/j.pnmrs.2019.10.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy of oriented samples makes accessible residual anisotropic intramolecular NMR interactions, such as chemical shift anisotropy (RCSA), dipolar coupling (RDC), and quadrupolar coupling (RQC), while preserving high spectral resolution. In addition, in a chiral aligned environment, enantiomers of chiral molecules or enantiopic elements of prochiral compounds adopt different average orientations on the NMR timescale, and hence produce distinct NMR spectra or signals. NMR spectroscopy in chiral aligned media is a powerful analytical tool, and notably provides unique information on (pro)chirality analysis, natural isotopic fractionation, stereochemistry, as well as molecular conformation and configuration. Significant progress has been made in this area over the three last decades, particularly using polypeptide-based chiral liquid crystals (CLCs) made of organic solutions of helically chiral polymers (as PBLG) in organic solvents. This review presents an overview of NMR in polymeric LCs. In particular, we describe the theoretical tools and the major NMR methods that have been developed and applied to study (pro)chiral molecules dissolved in such oriented solvents. We also discuss the representative applications illustrating the analytical potential of this original NMR tool. This overview article is dedicated to thirty years of original contributions to the development of NMR spectroscopy in polypeptide-based chiral liquid crystals.
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Affiliation(s)
- Philippe Lesot
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France; Centre National de la Recherche Scientifique (CNRS), France.
| | - Christie Aroulanda
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Philippe Berdagué
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Abdelkrim Meddour
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Denis Merlet
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Jonathan Farjon
- Centre National de la Recherche Scientifique (CNRS), France; Faculté des Sciences et Techniques de Nantes, UMR CNRS 6230, Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, CEISAM, Equipe EBSI, BP 92208, 2 rue de la Houssinière, F-44322 Nantes cedex 3, France
| | - Nicolas Giraud
- Université Paris Descartes, Sorbonne Paris Cité, UMR CNRS 8601, Laboratory of Pharmacological and Toxicological Chemistry and Biochemistry, LPTCB, 45 rue des Saints Pères, F-75006 Paris, France
| | - Olivier Lafon
- Universite de Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR CNRS 8181, Unité de Catalyse et Chimie du Solide, UCCS, F-59000 Lille, France; Institut Universitaire de France (IUF), France
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38
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Koos MRM, Navarro‐Vázquez A, Anklin C, Gil RR. Computer‐Assisted 3D Structure Elucidation (CASE‐3D): The Structural Value of
2
J
CH
in Addition to
3
J
CH
Coupling Constants. Angew Chem Int Ed Engl 2020; 59:3938-3941. [DOI: 10.1002/anie.201915103] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
| | | | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
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39
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Tzvetkova P, Sternberg U, Gloge T, Navarro-Vázquez A, Luy B. Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints. Chem Sci 2019; 10:8774-8791. [PMID: 31803450 PMCID: PMC6849632 DOI: 10.1039/c9sc01084j] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/19/2019] [Indexed: 12/27/2022] Open
Abstract
Residual dipolar couplings (RDCs) and other residual anisotropic NMR parameters provide valuable structural information of high quality and quantity, bringing detailed structural models of flexible molecules in solution in reach. The corresponding data interpretation so far is directly or indirectly based on the concept of a molecular alignment tensor, which, however, is ill-defined for flexible molecules. The concept is typically applied to a single or a small set of lowest energy structures, ignoring the effect of vibrational averaging. Here, we introduce an entirely different approach based on time averaged molecular dynamics with dipolar couplings as tensorial orientational restraints that can be used to solve structural problems in molecules of any size without the need of introducing an explicit molecular alignment tensor into the computation. RDC restraints are represented by their full 3D interaction tensor in the laboratory frame, for which pseudo forces are calculated using a secular dipolar Hamiltonian as the target. The resulting rotational averaging of each individual tensorial restraint leads to structural ensembles that best fulfil the experimental data. Using one-bond RDCs, the approach has been implemented in the force field procedures of the program COSMOS and extensively tested. A concise theoretical introduction, including the special treatment of force fields for stable and fast MD simulations, as well as applications regarding configurational analyses of small to medium-sized organic molecules with different degrees of flexibility, is given. The observed results are discussed in detail.
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Affiliation(s)
- Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Ulrich Sternberg
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Thomas Gloge
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Armando Navarro-Vázquez
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
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40
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Yan P, Li G, Wang C, Wu J, Sun Z, Martin GE, Wang X, Reibarkh M, Saurí J, Gustafson KR. Characterization by Empirical and Computational Methods of Dictyospiromide, an Intriguing Antioxidant Alkaloid from the Marine Alga Dictyota coriacea. Org Lett 2019; 21:7577-7581. [PMID: 31539931 PMCID: PMC7487124 DOI: 10.1021/acs.orglett.9b02856] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The challenging structural motif of dictyospiromide (1), a spirosuccinimide alkaloid with antioxidant properties that are associated with activation of the Nrf2/ARE signaling pathway, was assigned using contemporary NMR experiments complemented with anisotropic NMR, chiroptical, and computational methodologies. Anisotropic NMR parameters provided critical orthogonal verification of the configuration of the difficult to assign spiro carbon and the other stereogenic centers in 1.
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Affiliation(s)
- Pengcheng Yan
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People’s Republic of China
| | - Ge Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People’s Republic of China
| | - Chaojie Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People’s Republic of China
| | - Jianzhang Wu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People’s Republic of China
| | - Zhongmin Sun
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People’s Republic of China
| | - Gary E. Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey 07079, United States
| | - Xiao Wang
- Structure Elucidation Group, Analytical Research and Development, Merck & Co., Rahway, New Jersey 07065, United States
| | - Mikhail Reibarkh
- Structure Elucidation Group, Analytical Research and Development, Merck & Co., Rahway, New Jersey 07065, United States
| | - Josep Saurí
- Structure Elucidation Group, Analytical Research and Development, Merck & Co., Boston, Massachusetts 02115, United States
| | - Kirk R. Gustafson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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41
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Kutateladze AG, Holt T. Structure Validation of Complex Natural Products: Time to Change the Paradigm. What did Synthesis of Alstofolinine A Prove? J Org Chem 2019; 84:8297-8299. [DOI: 10.1021/acs.joc.9b00969] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrei G. Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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42
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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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43
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Ndukwe IE, Brunskill A, Gauthier DR, Zhong YL, Martin GE, Williamson RT, Reibarkh M, Liu Y. 13C NMR-Based Approaches for Solving Challenging Stereochemical Problems. Org Lett 2019; 21:4072-4076. [PMID: 31117703 DOI: 10.1021/acs.orglett.9b01248] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining the configuration of proton-deficient molecules is challenging using conventional NMR methods including nuclear Overhauser effect (NOE) and the proton-dependent J-based configuration analysis (JBCA). The problem is exacerbated when only one stereoisomer is available. Alternative methods based on the utilization of 13C NMR chemical shifts, 13C-13C homonuclear couplings measured at natural abundance, and residual chemical shift anisotropy measurements in conjunction with density functional theory calculations are illustrated with a proton-deficient model compound.
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Affiliation(s)
- Ikenna E Ndukwe
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Andrew Brunskill
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Donald R Gauthier
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Yong-Li Zhong
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Gary E Martin
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - R Thomas Williamson
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Mikhail Reibarkh
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
| | - Yizhou Liu
- Analytical Research & Development , Merck & Co. Inc. , Rahway , New Jersey 07065 , United States
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44
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Nugroho AE, Morita H. Computationally-assisted discovery and structure elucidation of natural products. J Nat Med 2019; 73:687-695. [PMID: 31093833 PMCID: PMC6713678 DOI: 10.1007/s11418-019-01321-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
Computer hardware development coupled with the development of quantum chemistry, new computational models and algorithms, and user-friendly interfaces have lowered the barriers to the use of computation in the discovery and structure elucidation of natural products. Consequently, the use of computational chemistry software as a tool to discover and determine the structure of natural products has become more common in recent years. In this review, we provide several examples of recent studies that used computer technology to facilitate the discovery and structure determination of various natural products.
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Affiliation(s)
- Alfarius Eko Nugroho
- Faculty of Pharmaceutical Sciences, Hoshi University, Ebara 2-4-41 Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Hiroshi Morita
- Faculty of Pharmaceutical Sciences, Hoshi University, Ebara 2-4-41 Shinagawa-ku, Tokyo, 142-8501, Japan.
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45
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Carvalho DS, da Silva DGB, Hallwass F, Navarro-Vázquez A. Chemically cross-linked polyacrylonitrile. A DMSO compatible NMR alignment medium for measurement of residual dipolar couplings and residual chemical shift anisotropies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 302:21-27. [PMID: 30933840 DOI: 10.1016/j.jmr.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/09/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
Chemically cross-linked polyacrylontrile polymer gels, have been prepared as an alignment medium compatible with DMSO-d6. These gels allow measurement of residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) with good accuracy as tested with brucine and α-santonin natural compounds. The gels can be reversibly compressed allowing easy measurement of RCSAs. They also present good physical homogeneity, clean HSQC spectra with little background 1H signals, and allow unambiguous referencing of 13C spectra for RCSA extraction.
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Affiliation(s)
- Daiane S Carvalho
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil
| | - Danilo G B da Silva
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil
| | - Fernando Hallwass
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil
| | - Armando Navarro-Vázquez
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco 50670-901, Brazil.
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46
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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.
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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
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47
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Lesot P, Berdagué P, Meddour A, Kreiter A, Noll M, Reggelin M. 2 H and 13 C NMR-Based Enantiodetection Using Polyacetylene versus Polypeptide Aligning Media: Versatile and Complementary Tools for Chemists. Chempluschem 2019; 84:144-153. [PMID: 31950698 DOI: 10.1002/cplu.201800493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Indexed: 12/12/2022]
Abstract
In this work, the practical/analytical potential of an L-valine-derived polyacetylene (PLA) lyotropic liquid crystal (LLC) is examined to spectrally discriminate enantiomers (racemic mixture) or enantiotopic directions of a large collection (23) of (pro)chiral model compounds (from rigid to flexible and polar to apolar ones), thus covering various important aspects of enantiomorphism. Experimental 2 H-{1 H} (deuterated analytes and at natural abundance level) and 13 C-{1 H} NMR results are discussed in terms of the difference of 2 H-RQCs or 13 C-RCSAs and compared to those obtained in polypeptide-type LLCs (PBLG). The analysis of the NMR results provides an overview of the enantiodifferentiation capabilities of PLA and gives useful/practical hints for the chemist to select the most appropriate chiral oriented system. Astonishing NAD NMR results were obtained in the case of one of the simplest, chiral alkanes, 3-methylhexane. From a theoretical viewpoint, the data collected highlight the key molecular factors involved in orientation/discrimination processes, as a basis for optimizing computational prediction (molecular dynamics simulation), as well as designing novel helically chiral polymers as new enantiodiscriminating aligning media. In addition, a new, robust and efficient protocol to synthesize PLA and its enantiomer (PDA) on a large scale and with small polydispersities is proposed.
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Affiliation(s)
- Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Sud/Université Paris-Saclay, Bât. 410, 91405, Orsay cedex, France
| | - Philippe Berdagué
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Sud/Université Paris-Saclay, Bât. 410, 91405, Orsay cedex, France
| | - Abdelkrim Meddour
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Sud/Université Paris-Saclay, Bât. 410, 91405, Orsay cedex, France
| | - Alexander Kreiter
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
| | - Markus Noll
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
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48
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Menna M, Imperatore C, Mangoni A, Della Sala G, Taglialatela-Scafati O. Challenges in the configuration assignment of natural products. A case-selective perspective. Nat Prod Rep 2019; 36:476-489. [DOI: 10.1039/c8np00053k] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An overview by a case study approach on the currently available methods for the configurational analysis of natural products.
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Affiliation(s)
- Marialuisa Menna
- Department of Pharmacy
- University of Naples Federico II
- 80131 Napoli
- Italy
| | | | - Alfonso Mangoni
- Department of Pharmacy
- University of Naples Federico II
- 80131 Napoli
- Italy
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49
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Ndukwe IE, Wang X, Pelczer I, Reibarkh M, Williamson RT, Liu Y, Martin GE. PBLG as a versatile liquid crystalline medium for anisotropic NMR data acquisition. Chem Commun (Camb) 2019; 55:4327-4330. [DOI: 10.1039/c9cc01130g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The chiral nematic phase of poly-γ-benzyl-l-glutamate (PBLG) formed in a chloroform–DMSO co-solvent system can be used as a versatile alignment medium for the acquisition of high quality anisotropic NMR data for molecules of varying polarities.
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Affiliation(s)
- Ikenna E. Ndukwe
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | - Xiao Wang
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | | | - Mikhail Reibarkh
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | | | - Yizhou Liu
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | - Gary E. Martin
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
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50
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Burns DC, Mazzola EP, Reynolds WF. The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products. Nat Prod Rep 2019; 36:919-933. [DOI: 10.1039/c9np00007k] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer-assisted structure elucidation can help to determine the structures of complex natural products while minimizing the risk of structure errors.
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Affiliation(s)
- Darcy C. Burns
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
| | - Eugene P. Mazzola
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
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