1
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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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2
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Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2 N-1 Diastereomers. JOURNAL OF NATURAL PRODUCTS 2022; 85:1837-1849. [PMID: 35820115 DOI: 10.1021/acs.jnatprod.2c00427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.
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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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3
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Li XL, Ru T, Navarro-Vázquez A, Lindemann P, Nazaré M, Li XW, Guo YW, Sun H. Weizhouochrones: Gorgonian-Derived Symmetric Dimers and Their Structure Elucidation Using Anisotropic NMR Combined with DP4+ Probability and CASE-3D. JOURNAL OF NATURAL PRODUCTS 2022; 85:1730-1737. [PMID: 35792821 DOI: 10.1021/acs.jnatprod.2c00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Natural product dimers have intriguing structural features and often have remarkable pharmacological activities. We report here two uncommon marine gorgonian-derived symmetric dimers, weizhouochrones A (1) and B (2), with indenone-derived monomers, that were isolated from the coral Anthogorgia ochracea collected from the South China Sea. These dimers are difficult targets for structure elucidation that solely relies upon conventional NMR data such as NOEs and J-couplings. Here, to explore the application of emerging methods on the structure elucidation of challenging molecules, we explored a number of different anisotropic and computational NMR approaches. The measurements of anisotropic NMR parameters of weizhouochrone A, including residual dipolar couplings (RDCs) and residual chemical shift anisotropy (RCSA), allowed us to successfully determine the planar structure and its relative configuration. This result was corroborated by a computational NMR analysis based on DP4+ probability and computer-assisted 3D structure elucidation (CASE-3D).
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Affiliation(s)
- Xiao-Lu Li
- Group of Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Tong Ru
- 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
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Peter Lindemann
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Marc Nazaré
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Han Sun
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
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4
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Schirra DS, Jeziorowski S, Lehmann M, Thiele CM. Thermoreversible Gelation of Homopolyglutamates PBPMLG, PBPELG, and PBPHLG: Another Step toward de Novo RDC-Based Structure Elucidation. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dominic S. Schirra
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Sharon Jeziorowski
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Matthias Lehmann
- Institute for Organic Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
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5
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Wesp S, Wolf K, Immel S, Reggelin M. Poly(arylisocyanides) as Versatile, Enantiodiscriminating Alignment Media for Small Molecules. Chempluschem 2022; 87:e202100507. [PMID: 35072980 DOI: 10.1002/cplu.202100507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/02/2022] [Indexed: 11/08/2022]
Abstract
Lyotropic liquid crystalline (LLC) phases of amino acid derived polyarylisocyanides were employed as chiral alignment media for the measurement of residual dipolar couplings (RDCs) of small chiral organic molecules. Anisotropic samples in CDCl3 displayed quadrupolar splittings of the deuterium signal in the range of several hundreds of Hertz. The LLC phases showed excellent orienting properties for a broad range of analytes bearing various functional groups. The precise extraction of RDCs in the range of up to ±40 Hertz from F2-coupled HSQC spectra was possible. Additionally, the chiral environment offers the opportunity for diastereomorphous interactions with the enantiomers of chiral analytes leading to two different sets of RDCs. This differential order effect was particularly pronounced with ketones and alcohols.
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Affiliation(s)
- Svenja Wesp
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Kai Wolf
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Stefan Immel
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
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6
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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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7
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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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8
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Köck M, Reggelin M, Immel S. Model-Free Approach for the Configurational Analysis of Marine Natural Products. Mar Drugs 2021; 19:md19060283. [PMID: 34063741 PMCID: PMC8223791 DOI: 10.3390/md19060283] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/17/2022] Open
Abstract
The NMR-based configurational analysis of complex marine natural products is still not a routine task. Different NMR parameters are used for the assignment of the relative configuration: NOE/ROE, homo- and heteronuclear J couplings as well as anisotropic parameters. The combined distance geometry (DG) and distance bounds driven dynamics (DDD) method allows a model-free approach for the determination of the relative configuration that is invariant to the choice of an initial starting structure and does not rely on comparisons with (DFT) calculated structures. Here, we will discuss the configurational analysis of five complex marine natural products or synthetic derivatives thereof: the cis-palau’amine derivatives 1a and 1b, tetrabromostyloguanidine (1c), plakilactone H (2), and manzamine A (3). The certainty of configurational assignments is evaluated in view of the accuracy of the NOE/ROE data available. These case studies will show the prospective breadth of application of the DG/DDD method.
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Affiliation(s)
- Matthias Köck
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Correspondence: (M.K.); (S.I.)
| | - Michael Reggelin
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany;
| | - Stefan Immel
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany;
- Correspondence: (M.K.); (S.I.)
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9
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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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10
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Reggelin M, Immel S. Configurational Analysis by Residual Dipolar Couplings: Critical Assessment of "Structural Noise" from Thermal Vibrations. Angew Chem Int Ed Engl 2021; 60:3412-3416. [PMID: 33137233 PMCID: PMC7898695 DOI: 10.1002/anie.202011081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Indexed: 12/11/2022]
Abstract
The certainty of configurational assignments of natural products based on anisotropic NMR parameters, such as residual dipolar couplings (RDCs), must be amended by estimates on structural noise emerging from thermal vibrations. We show that vibrational analysis significantly affects the error margins with which RDCs can be back-calculated from molecular models, and the implications of thermal motions on the differentiability of diastereomers are derived.
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Affiliation(s)
- Michael Reggelin
- Technische Universität DarmstadtClemens Schöpf Institut für Organische Chemie und BiochemieAlarich-Weiss-Strasse 464287DarmstadtGermany
| | - Stefan Immel
- Technische Universität DarmstadtClemens Schöpf Institut für Organische Chemie und BiochemieAlarich-Weiss-Strasse 464287DarmstadtGermany
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11
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Reggelin M, Immel S. Configurational Analysis by Residual Dipolar Couplings: Critical Assessment of “Structural Noise” from Thermal Vibrations. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Reggelin
- Technische Universität Darmstadt Clemens Schöpf Institut für Organische Chemie und Biochemie Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Stefan Immel
- Technische Universität Darmstadt Clemens Schöpf Institut für Organische Chemie und Biochemie Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
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12
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Köck M, Reggelin M, Immel S. The Advanced Floating Chirality Distance Geometry Approach-How Anisotropic NMR Parameters Can Support the Determination of the Relative Configuration of Natural Products. Mar Drugs 2020; 18:md18060330. [PMID: 32599876 PMCID: PMC7344786 DOI: 10.3390/md18060330] [Citation(s) in RCA: 6] [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: 05/04/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 11/16/2022] Open
Abstract
The configurational analysis of complex natural products by NMR spectroscopy is still a challenging task. The assignment of the relative configuration is usually carried out by analysis of interproton distances from NOESY or ROESY spectra (qualitative or quantitative) and scalar (J) couplings. About 15 years ago, residual dipolar couplings (RDCs) were introduced as a tool for the configurational determination of small organic molecules. In contrast to NOEs/ROEs which are local parameters (distances up to 400 pm can be detected for small organic molecules), RDCs are global parameters which allow to obtain structural information also from long-range relationships. RDCs have the disadvantage that the sample needs a setup in an alignment medium in order to obtain the required anisotropic environment. Here, we will discuss the configurational analysis of five complex natural products: axinellamine A (1), tetrabromostyloguanidine (2), 3,7-epi-massadine chloride (3), tubocurarine (4), and vincristine (5). Compounds 1-3 are marine natural products whereas 4 and 5 are from terrestrial sources. The chosen examples will carefully work out the limitations of NOEs/ROEs in the configurational analysis of natural products and will also provide an outlook on the information obtained from RDCs.
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Affiliation(s)
- 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
| | - Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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13
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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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14
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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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15
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Navarro-Vázquez A. When not to rely on Boltzmann populations. Automated CASE-3D structure elucidation of hyacinthacines through chemical shift differences. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:139-144. [PMID: 31663628 DOI: 10.1002/mrc.4951] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/03/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
An Akaike Information Criterion (AIC) procedure (CASE-3D) has been successfully applied to the NMR based configurational assignment of reported hyacinthacines (1-3,5-8), recently target of configurational analysis using the popular DP4+ methodology. The present analysis makes use of reported 1 H and 13 C shifts and, in some particular cases, a few 3 JHH couplings. The difficulty in proper computational prediction of relative energies, in molecules capable of inter-molecular hydrogen bonding, introduces large errors in the prediction of conformationally averaged NMR properties in methods based on Boltzmann averaging such as DP4 or DP4+. In contrast CASE-3D conformational amplitudes are free parameters in the model. Here we show that the CASE-3D conformational model selection strategy, when combined with a larger energy cutoff in the molecular-modelling conformational exploration, was sufficient to correctly assign the relative configuration in five of seven cases. Introduction of more information, either by supplementing 1 H and 13 C data with a few J-couplings, or using a cutoff based on computed DFT energies for the definition of the conformational ensembles, allowed the safe assignment of configuration for all compounds.
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Affiliation(s)
- Armando Navarro-Vázquez
- Universidade Federal de Pernambuco, Departamento de Química Fundamental, CCEN, Recife, Pernambuco, Brazil, 50670-90.1
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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: 36] [Impact Index Per Article: 9.0] [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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