1
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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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2
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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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3
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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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4
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil-Silva LF, Gil RR. Cross-Linked Poly-4-Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021; 60:26314-26319. [PMID: 34609778 DOI: 10.1002/anie.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/07/2022]
Abstract
Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross-linked poly-4-acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) and J-coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α-helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure-based drug design.
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Affiliation(s)
- Kathleen A Farley
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Martin R M Koos
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Ye Che
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Reto Horst
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Chris Limberakis
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Justin Bellenger
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Ricardo Lira
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | | | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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5
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil‐Silva LF, Gil RR. Cross‐Linked Poly‐4‐Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
| | - Ye Che
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Reto Horst
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Chris Limberakis
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Justin Bellenger
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Ricardo Lira
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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Abstract
Many natural products have been used as drugs for the treatment of diverse indications. Although most U.S. pharmaceutical companies have reduced or eliminated their in-house natural-product research over the years, new approaches for compound screening and chemical synthesis are resurrecting interest in exploring the therapeutic value of natural products. The aim of this commentary is to review emerging strategies and techniques that have made natural products a viable strategic choice for inclusion in drug discovery programs. Published 2019. U.S. Government.
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Affiliation(s)
- John A Beutler
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
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16
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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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17
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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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18
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Wu Q, Ye F, Li XL, Liang LF, Sun J, Sun H, Guo YW, Wang H. Uncommon Polyoxygenated Sesquiterpenoids from South China Sea Soft Coral Lemnalia flava. J Org Chem 2019; 84:3083-3092. [PMID: 30762361 DOI: 10.1021/acs.joc.8b02912] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A detailed chemical investigation of the Chinese soft coral Lemnalia flava yielded four new nardosinane-type sesquiterpenoids (1-4), one new neolemnane-type sesquiterpenoid (5), and one new sesquiterpenoid with an uncommon 6/9 fused bicyclic skeleton (6), together with two known related compounds (7 and 8). The structures and absolute configurations of 1-8 were determined on the basis of extensive spectroscopic data analyses, X-ray diffraction analysis, chemical reactions, and computer-assisted structural elucidation including 13C NMR data calculation, residual dipolar coupling based NMR analysis, and time-dependent density functional theoryelectronic circular dichroism calculation. Plausible biogenetic pathways of two uncommon sesquiterpenoids (4 and 6) were proposed.
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Affiliation(s)
- Qihao Wu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals , Zhejiang University of Technology , Hangzhou , China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zu Chong Zhi Road , Zhangjiang Hi-Tech Park, Shanghai 201203 , China
| | - Fei Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zu Chong Zhi Road , Zhangjiang Hi-Tech Park, Shanghai 201203 , China
| | - Xiao-Lu Li
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , Berlin 13125 , Germany
| | - Lin-Fu Liang
- College of Material Science and Engineering , Central South University of Forestry and Technology , Changsha 410004 , China
| | - Jiadong Sun
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Han Sun
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , Berlin 13125 , Germany
| | - Yue-Wei Guo
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals , Zhejiang University of Technology , Hangzhou , China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zu Chong Zhi Road , Zhangjiang Hi-Tech Park, Shanghai 201203 , China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals , Zhejiang University of Technology , Hangzhou , China
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19
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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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20
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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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21
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Application of anisotropic NMR parameters to the confirmation of molecular structure. Nat Protoc 2018; 14:217-247. [DOI: 10.1038/s41596-018-0091-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Liu Y, Cohen RD, Martin GE, Williamson RT. A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 291:63-72. [PMID: 29723716 DOI: 10.1016/j.jmr.2018.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Accurate measurement of residual dipolar couplings (RDCs) requires an appropriate degree of alignment in order to optimize data quality. An overly weak alignment yields very small anisotropic data that are susceptible to measurement errors, whereas an overly strong alignment introduces extensive anisotropic effects that severely degrade spectral quality. The ideal alignment amplitude also depends on the specific pulse sequence used for the coupling measurement. In this work, we introduce a practical strategy for the accurate measurement of one-bond 13C-1H RDCs up to a range of ca. -300 to +300 Hz, corresponding to an alignment that is an order of magnitude stronger than typically employed for small molecule structural elucidation. This strong alignment was generated in the mesophase of the commercially available poly-γ-(benzyl-L-glutamate) polymer. The total coupling was measured by the simple and well-studied heteronuclear two-dimensional J-resolved experiment, which performs well in the presence of strong anisotropic effects. In order to unequivocally determine the sign of the total coupling and resolve ambiguities in assigning total couplings in the CH2 group, coupling measurements were conducted at an isotropic condition plus two anisotropic conditions of different alignment amplitudes. Most RDCs could be readily extracted from these measurements whereas more complicated spectral effects resulting from strong homonuclear coupling could be interpreted either theoretically or by simulation. Importantly, measurement of these very large RDCs actually offers significantly improved data quality and utility for the structure determination of small organic molecules.
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Affiliation(s)
- Yizhou Liu
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co. Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA.
| | - Ryan D Cohen
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co. Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA
| | - Gary E Martin
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co. Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA
| | - R Thomas Williamson
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co. Inc., 126 East Lincoln Avenue, Rahway, NJ 07065, USA
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