1
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Sternberg U, Tichotová MC, Tučková L, Ešnerová A, Hanus J, Baszczyňski O, Procházková E. Extending molecular dynamics with dipolar NMR tensors as constraints to chiral phosphorus compounds. Phys Chem Chem Phys 2024; 26:20814-20819. [PMID: 39044477 DOI: 10.1039/d4cp02401j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Molecular dynamics with orientational constraints (MDOC) simulations use NMR parameters as tensorial constraints in the stereochemical analysis of small molecules. 13C-31P Residual dipolar couplings-aided MDOC simulations of small phosphorus molecules determined the relative configurations of rigid molecules after including 3JH-H-couplings as additional constraints. However, flexible molecules remain a problem.
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Affiliation(s)
- Ulrich Sternberg
- COSMOS-Software, 07743 Jena, Germany
- Karlsruhe Institute of Technology (KIT), Postfach 3640, D-76021 Karlsruhe, Germany
| | - Markéta Christou Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
| | - Aneta Ešnerová
- Department of Organic Chemistry, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Jan Hanus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
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2
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Tichotová M, Landovský T, Lang J, Jeziorowski S, Schmidts V, Kohout M, Babor M, Lhoták P, Thiele CM, Dvořáková H. Enantiodiscrimination of Inherently Chiral Thiacalixarenes by Residual Dipolar Couplings. J Org Chem 2024; 89:9711-9720. [PMID: 36655948 PMCID: PMC11267606 DOI: 10.1021/acs.joc.2c02594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Indexed: 01/20/2023]
Abstract
Inherently chiral compounds, such as calixarenes, are chiral due to a nonplanar three-dimensional (3D) structure. Determining their conformation is essential to understand their properties, with nuclear magnetic resonance (NMR) spectroscopy being one applicable method. Using alignment media to measure residual dipolar couplings (RDCs) to obtain structural information is advantageous when classical NMR parameters like the nuclear Overhauser effect (NOE) or J-couplings fail. Besides providing more accurate structural information, the alignment media can induce different orientations of enantiomers. In this study, we examined the ability of polyglutamates with different side-chain moieties─poly-γ-benzyl-l-glutamate (PBLG) and poly-γ-p-biphenylmethyl-l-glutamate (PBPMLG) ─to enantiodifferentiate the inherently chiral phenoxathiin-based thiacalix[4]arenes. Both media, in combination with two solvents, allowed for enantiodiscrimination, which was, to the best of our knowledge, proved for the first time on inherently chiral compounds. Moreover, using the experimental RDCs, we investigated the calix[4]arenes conformational preferences in solution, quantitatively analyzed the differences in the alignment of the enantiomers, and discussed the pitfalls of the use of the RDC analysis.
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Affiliation(s)
- Markéta Tichotová
- Laboratory
of NMR Spectroscopy, University of Chemistry
and Technology Prague (UCTP), Technická 5, 166 28Prague 6, Czech Republic
- Department
of Physical and Macromolecular Chemistry, Charles University, Hlavova 8, 128 00Prague 2, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo náměstí 542, 160 00Prague 6, Czech Republic
| | - Tomáš Landovský
- Department
of Organic Chemistry, University of Chemistry
and Technology Prague (UCTP), Technická 5, 166 28Prague 6, Czech Republic
| | - Jan Lang
- Faculty
of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16Prague 2, Czech Republic
| | - Sharon Jeziorowski
- Department
of Chemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 16, 64287Darmstadt, Germany
| | - Volker Schmidts
- Department
of Chemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 16, 64287Darmstadt, Germany
| | - Michal Kohout
- Department
of Organic Chemistry, University of Chemistry
and Technology Prague (UCTP), Technická 5, 166 28Prague 6, Czech Republic
| | - Martin Babor
- Department
of Solid State Chemistry, University of
Chemistry and Technology Prague (UCTP), Technická 5, 166 28Prague 6, Czech Republic
| | - Pavel Lhoták
- Department
of Organic Chemistry, University of Chemistry
and Technology Prague (UCTP), Technická 5, 166 28Prague 6, Czech Republic
| | - Christina M. Thiele
- Department
of Chemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 16, 64287Darmstadt, Germany
| | - Hana Dvořáková
- Laboratory
of NMR Spectroscopy, University of Chemistry
and Technology Prague (UCTP), Technická 5, 166 28Prague 6, Czech Republic
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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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Tichotová MC, Tučková L, Kocek H, Růžička A, Straka M, Procházková E. Exploring the impact of alignment media on RDC analysis of phosphorus-containing compounds: a molecular docking approach. Phys Chem Chem Phys 2024; 26:2016-2024. [PMID: 38126374 DOI: 10.1039/d3cp04099b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Residual dipolar couplings (RDCs) are employed in NMR analysis when conventional methods, such as J-couplings and nuclear Overhauser effects (NOEs) fail. Low-energy (optimized) conformers are often used as input structures in RDC analysis programs. However, these low-energy structures do not necessarily resemble conformations found in anisotropic environments due to interactions with the alignment medium, especially if the analyte molecules are flexible. Considering interactions with alignment media in RDC analysis, we developed and evaluated a molecular docking-based approach to generate more accurate conformer ensembles for compounds in the presence of the poly-γ-benzyl-L-glutamate alignment medium. We designed chiral phosphorus-containing compounds that enabled us to utilize 31P NMR parameters for the stereochemical analysis. Using P3D/PALES software to evaluate diastereomer discrimination, we found that our conformer ensembles outperform moderately the standard, low-energy conformers in RDC analysis. To further improve our results, we (i) averaged the experimental values of the molecular docking-based conformers by applying the Boltzmann distribution and (ii) optimized the structures through normal mode relaxation, thereby enhancing the Pearson correlation factor R and even diastereomer discrimination in some cases. Nevertheless, we presume that significant differences between J-couplings in isotropic and in anisotropic environments may preclude RDC measurements for flexible molecules. Therefore, generating conformer ensembles based on molecular docking enhances RDC analysis for mildly flexible systems while flexible molecules may require applying more advanced approaches, in particular approaches including dynamical effects.
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Affiliation(s)
- Markéta Christou Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Hugo Kocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice 532 10, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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5
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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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6
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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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7
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Roth FA, Schmidts V, Thiele CM. TITANIA: Model-Free Interpretation of Residual Dipolar Couplings in the Context of Organic Compounds. J Org Chem 2021; 86:15387-15402. [PMID: 34677977 DOI: 10.1021/acs.joc.1c01926] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) become increasingly important as additional NMR parameters in the structure elucidation of organic compounds but are usually used in fitting procedures to discriminate between (computed) structures that are in accordance with RDCs and others that can be ruled out. Thus, the determination of configurations requires prior structural information. The direct use of RDCs as restraints to construct structures based on RDCs has only recently begun also in organic compounds. No protocol has been published though that uses the vector and dynamics information available in multialignment data sets directly for the joint determination of conformation and configuration of organic compounds. This is proposed in the current study. We show that by employing these data, even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. The requirements in terms of the number of RDCs and alignment media necessary are discussed in detail.
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Affiliation(s)
- Felix A Roth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
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8
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Krupp A, Noll M, Reggelin M. Valine derived poly (acetylenes) as versatile chiral lyotropic liquid crystalline alignment media for RDC-based structure elucidations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:577-586. [PMID: 32012341 DOI: 10.1002/mrc.5003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Anisotropic samples of lyotropic liquid crystalline (LLC) phases of valine derived polyaryl acetylenes were employed as chiral alignment media for the measurement of residual dipolar couplings (RDCs) of 12 small, chiral, organic molecules. The quadrupolar splitting of the deuterium signal of CDCl3 can be adjusted by temperature and concentration changes from 0 to 350 Hz. The LLC phases showed excellent orienting properties for all analytes bearing various functional groups. The precise extraction of RDCs in the range of up to ±30 Hz from F2-coupled HSQC spectra was possible. Additionally, the chiral environment led to diastereomorphous interactions with the enantiomers of chiral analytes leading to two different sets of RDCs. This differential order effect was particularly pronounced with H-bond donors like alcohols and 2° amines.
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Affiliation(s)
- Alexis Krupp
- Clemens Schöpf Institut for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
- Nitrochemie Aschau GmbH, Aschau am Inn, Germany
| | - Markus Noll
- Clemens Schöpf Institut for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Michael Reggelin
- Clemens Schöpf Institut for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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9
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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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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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Sternberg U, Tzvetkova P, Muhle-Goll C. The simulation of NMR data of flexible molecules: sagittamide A as an example for MD simulations with orientational constraints. Phys Chem Chem Phys 2020; 22:17375-17384. [PMID: 32705098 DOI: 10.1039/d0cp01905d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recently developed MDOC (Molecular Dynamics with Orientational Constraints) simulation is applied for the first time to a fully flexible molecule. MDOC simulations aim to single out the naturally existing configuration of molecules and to elucidate conformer populations. The performance of the method was first demonstrated on a well-studied test case, the five-membered ring lactone (α-methylene-γ-butyrolactone). In the case of sagittamide A, one-bond 1H-13C residual dipolar couplings (RDC) are used as orientational constraints that reorient the molecule or parts of it. In addition, NOE distances and 3J scalar couplings are used as constraints. Five possible configurations of sagittamide A (labelled a to e) are considered. One experimental RDC value per flexible unit was available and this was not sufficient to single out one valid configuration. The problem could be solved by including NOE distances as well as 3J couplings as complementary constraints into the MDOC simulations. In accordance with former investigations, we confirmed the configuration a for the natural product. A detailed analysis of conformers of the central chain of 6 chiral carbon atoms could be given by inspecting the MDOC trajectory. The relative abundance of these conformers is crucial in fulfilling all three sets of constraints.
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Affiliation(s)
- Ulrich Sternberg
- Research Partner of Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. and COSMOS-Software, Jena, Germany
| | - Pavleta Tzvetkova
- Institute of Biological Interfaces 4, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute of Biological Interfaces 4, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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12
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Alcaraz Janßen M, Thiele CM. Poly-γ-S-perillyl-l-glutamate and Poly-γ-S-perillyl-d-glutamate: Diastereomeric Alignment Media Used for the Investigation of the Alignment Process. Chemistry 2020; 26:7831-7839. [PMID: 32134524 PMCID: PMC7384199 DOI: 10.1002/chem.201905447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Indexed: 11/09/2022]
Abstract
Residual dipolar couplings (RDCs) offer additional information for structure elucidation by NMR spectroscopy. They are measured in anisotropic media, such as lyotropic liquid crystalline phases of polypeptides. Today, some suitable polypeptides are known. Nevertheless, structural influences of these polypeptides on the alignment properties are not really understood. Thus, which influence a chiral side chain has on enantiodiscrimination and whether we can improve the enantiodifferentiation significantly by adding an additional chiral center in the side chain are questions of interest. Therefore, new diastereomeric polypeptide-based alignment media with an additional chiral center in the side chain derived from perillyl alcohol were synthesized and their properties were investigated (secondary structure, liquid crystallinity, etc.). The enantiomers of isopinocampheol and β-pinene were used as model analytes for the study of enantiodiscrimination. Additionally, the usage of 1 H-1 H-RDCs to improve the alignment tensor quality is demonstrated.
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Affiliation(s)
- Marcel Alcaraz Janßen
- Clemens-Schöpf-Institut für Organische Chemie und BiochemieTechnical University of DarmstadtAlarich-Weiss-Str. 1664287DarmstadtGermany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und BiochemieTechnical University of DarmstadtAlarich-Weiss-Str. 1664287DarmstadtGermany
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13
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Sinnaeve D, Ilgen J, Di Pietro ME, Primozic JJ, Schmidts V, Thiele CM, Luy B. Probing Long‐Range Anisotropic Interactions: a General and Sign‐Sensitive Strategy to Measure
1
H–
1
H Residual Dipolar Couplings as a Key Advance for Organic Structure Determination. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Davy Sinnaeve
- Univ. LilleInsermInstitut Pasteur de LilleCHU LilleU1167—Labex DISTALZ—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 59000 Lille France
- CNRS, ERL9002—Integrative Structural Biology 59000 Lille France
- Department of Organic and Macromolecular ChemistryGhent University, Campus Sterre, S4 Krijgslaan 281 9000 Ghent Belgium
| | - Julian Ilgen
- Clemens-Schöpf Institut für Organische Chemie und BiochemieTechnische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Maria Enrica Di Pietro
- Institute of Organic Chemistry and Institute for Biological Interfaces 4—Magnetic ResonanceKarlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Current address: Department of ChemistryMaterials and Chemical Engineering “Giulio Natta”Politecnico di Milano Piazza Leonardo da Vinci 32 20133 Milan Italy
| | - Johann J. Primozic
- Clemens-Schöpf Institut für Organische Chemie und BiochemieTechnische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Volker Schmidts
- Clemens-Schöpf Institut für Organische Chemie und BiochemieTechnische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Clemens-Schöpf Institut für Organische Chemie und BiochemieTechnische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4—Magnetic ResonanceKarlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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14
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Sinnaeve D, Ilgen J, Di Pietro ME, Primozic JJ, Schmidts V, Thiele CM, Luy B. Probing Long-Range Anisotropic Interactions: a General and Sign-Sensitive Strategy to Measure 1 H- 1 H Residual Dipolar Couplings as a Key Advance for Organic Structure Determination. Angew Chem Int Ed Engl 2020; 59:5316-5320. [PMID: 31945235 DOI: 10.1002/anie.201915278] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Indexed: 11/10/2022]
Abstract
Residual dipolar couplings (RDCs) are amongst the most powerful NMR parameters for organic structure elucidation. In order to maximize their effectiveness in increasingly complex cases such as flexible compounds, a maximum of RDCs between nuclei sampling a large distribution of orientations is needed, including sign information. For this, the easily accessible one-bond 1 H-13 C RDCs alone often fall short. Long-range 1 H-1 H RDCs are both abundant and typically sample highly complementary orientations, but accessing them in a sign-sensitive way has been severely obstructed due to the overflow of 1 H-1 H couplings. Here, we present a generally applicable strategy that allows the measurement of a large number of 1 H-1 H RDCs, including their signs, which is based on a combination of an improved PSYCHEDELIC method and a new selective constant-time β-COSY experiment. The potential of 1 H-1 H RDCs to better determine molecular alignment and to discriminate between enantiomers and diastereomers is demonstrated.
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Affiliation(s)
- Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167-Labex DISTALZ-RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, 59000, Lille, France.,CNRS, ERL9002-Integrative Structural Biology, 59000, Lille, France.,Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, S4, Krijgslaan 281, 9000, Ghent, Belgium
| | - Julian Ilgen
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Maria Enrica Di Pietro
- Institute of Organic Chemistry and Institute for Biological Interfaces 4-Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.,Current address: Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milan, Italy
| | - Johann J Primozic
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, 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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15
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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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16
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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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17
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Doppler A, Nicholls LDM, Golz C, Alcarazo M, John M. Orientation and conformation of two [6]carbohelicenes in stretched polystyrene and a thermoresponsive polyaspartate. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:961-967. [PMID: 31291475 DOI: 10.1002/mrc.4921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 06/09/2023]
Abstract
Two functionalized [6]carbohelicenes, one of which was also available in its two enantiomeric pure forms, were oriented in stretched polystyrene in CDCl3 , and in a recently introduced chiral thermoresponsive lyotropic polyaspartate (poly(benzyl)0.5 (phenethyl)0.5 -L-aspartate) in C2 D2 Cl4 . From the resulting 1 H,13 C residual dipolar couplings, the helical pitch of a methylated [6]carbohelicene was determined and found to be in agreement with theoretical predictions and existing crystal structures (d(C2,C2') ≈ 4.3 Å). For a second [6]carbohelicene with para-methoxyphenyl substituents, a clear conformational preference of the substituents was observed. The orientational properties of the two helicene enantiomers in the chiral polyaspartate are very similar, but both drastically change around 306 K. We suggest this behavior is due to an unusual phase transition in the liquid crystal.
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Affiliation(s)
- Anna Doppler
- Fakultät für Chemie, Georg-August-Universität, Göttingen, Germany
| | - Leo D M Nicholls
- Fakultät für Chemie, Georg-August-Universität, Göttingen, Germany
| | - Christopher Golz
- Fakultät für Chemie, Georg-August-Universität, Göttingen, Germany
| | - Manuel Alcarazo
- Fakultät für Chemie, Georg-August-Universität, Göttingen, Germany
| | - Michael John
- Fakultät für Chemie, Georg-August-Universität, Göttingen, Germany
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18
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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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19
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Di Pietro ME, Sternberg U, Luy B. Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules. J Phys Chem B 2019; 123:8480-8491. [PMID: 31502838 DOI: 10.1021/acs.jpcb.9b07008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The potential of residual dipolar couplings (RDCs) in conformational studies of small molecules is now widely recognized, but current theoretical approaches for their interpretation have several limitations and there is still the need for a general method to probe the torsional angle distributions applicable to any rotationally flexible molecule. Molecular dynamics simulations with RDC-based orientational tensorial constraints (MDOC), implemented in the software COSMOS, are presented here as a conceptually new strategy. For the cases of the fluorinated anti-inflammatory drug diflunisal and the disaccharide cellobiose, we demonstrate that MDOC simulations with one-bond RDCs as tensorial constraints unveil torsion distributions and allow the determination of relative configuration in the presence of rotational flexibility. The independence of the initial structure or any a priori assumption as well as the possibility to combine different experimental constraints represent features, which make the COSMOS software a promising tool for the investigation of torsional angle distributions of flexible molecules, regardless of their size and degree of freedom.
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Affiliation(s)
- Maria E Di Pietro
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Ulrich Sternberg
- COSMOS GbR , Jena 07743 , Germany.,Research Partner , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Burkhard Luy
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany.,Institute for Biological Interfaces 4-Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen 76021 , Germany
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20
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Knoll K, Leyendecker M, Thiele CM. l
‐Valine Derivatised 1,3,5‐Benzene‐Tricarboxamides as Building Blocks for a New Supramolecular Organogel‐Like Alignment Medium. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kevin Knoll
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
| | - Martin Leyendecker
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
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21
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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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22
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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23
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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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24
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Schwab M, Schmidts V, Thiele CM. Thermoresponsive Alignment Media in NMR Spectroscopy: Helix Reversal of a Copolyaspartate at Ambient Temperatures. Chemistry 2018; 24:14373-14377. [PMID: 29999196 DOI: 10.1002/chem.201803540] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 11/07/2022]
Abstract
Poly(aspartic acid esters) are known to form either right-or left-handed α-helices depending on the ester group in the side chain, on solvent and/or on temperature. Polyphenethyl-l-aspartates (PPLA) exhibit a helix reversal from the right- to the left-handed form with increasing temperature. We have recently reported the application of polyphenethylaspartates as helically chiral alignment media. The thermoresponsivity observed for these polymers offers the possibility to measure different orientations of analytes before and after helix reversal of the alignment medium at 373 K. Herein we present a synthesized copolymer of phenethyl- and benzylaspartate as a new alignment medium undergoing this helix reversal at 303-313 K. Thus, the measurement of residual dipolar couplings (RDC) before and after the helix reversal is allowed for at ambient temperatures. A complete sign change of all 1 H-13 C RDCs was observed, which is close to the highest possible difference in NMR spectra.
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Affiliation(s)
- Mira Schwab
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
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25
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Schwab M, Herold D, Thiele CM. Polyaspartates as Thermoresponsive Enantiodifferentiating Helically Chiral Alignment Media for Anisotropic NMR Spectroscopy. Chemistry 2017; 23:14576-14584. [DOI: 10.1002/chem.201702884] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Mira Schwab
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Dominik Herold
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
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26
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Rigling C, Ebert MO. RDC-enhanced structure calculation of a β-heptapeptide in methanol. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:655-661. [PMID: 27976817 DOI: 10.1002/mrc.4569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/06/2016] [Accepted: 12/12/2016] [Indexed: 05/28/2023]
Abstract
Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β-peptide with proteinogenic side chains in methanol. 1 DCH , 1 DNH , and 2 DHH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long-range definition in the backbone of the resulting 314 -helix and uncovers side-chain mobility. Experimental side-chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three-state model. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Carla Rigling
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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27
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Hansmann S, Schmidts V, Thiele CM. Synthesis of Poly-γ-S-2-methylbutyl-l-glutamate and Poly-γ-S-2-methylbutyl-d-glutamate and Their Use as Enantiodiscriminating Alignment Media in NMR Spectroscopy. Chemistry 2017; 23:9114-9121. [DOI: 10.1002/chem.201700699] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Stefanie Hansmann
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
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28
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Fredersdorf M, Kurz M, Bauer A, Ebert MO, Rigling C, Lannes L, Thiele CM. Conformational Analysis of an Antibacterial Cyclodepsipeptide Active against Mycobacterium tuberculosis
by a Combined ROE and RDC Analysis. Chemistry 2017; 23:5729-5735. [DOI: 10.1002/chem.201605143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Maic Fredersdorf
- Sanofi-Aventis GmbH; Department of Chemistry; Industriepark Hoechst 65926 Frankfurt am Main Germany
- Technische Universität Darmstadt; Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Michael Kurz
- Sanofi-Aventis GmbH; Department of Chemistry; Industriepark Hoechst 65926 Frankfurt am Main Germany
| | - Armin Bauer
- Sanofi-Aventis GmbH; Department of Chemistry; Industriepark Hoechst 65926 Frankfurt am Main Germany
| | - Marc-Olivier Ebert
- ETH Zürich; Laboratorium für Organische Chemie, D-CHAB; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Carla Rigling
- ETH Zürich; Laboratorium für Organische Chemie, D-CHAB; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Laurie Lannes
- Present address: Center for Biomolecular Magnetic Resonance; BMRZ); Institute of Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe Universität Frankfurt; Max-von-Laue-Straße 7 60438 Frankfurt Germany
| | - Christina Marie Thiele
- Technische Universität Darmstadt; Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
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29
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Moskalenko YE, Bagutski V, Thiele CM. Chemically synthesized and cross-linked PDMS as versatile alignment medium for organic compounds. Chem Commun (Camb) 2017; 53:95-98. [DOI: 10.1039/c6cc08762k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of PDMS gels with controlled amount of cross-linker opens up the opportunity for tuning of alignment media for RDC structure elucidation of organic molecules and mixtures of their isomers.
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Affiliation(s)
- Yulia E. Moskalenko
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- Technische Unitersität Darmstadt
- 64287 Darmstadt
- Germany
| | - Viktor Bagutski
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- Technische Unitersität Darmstadt
- 64287 Darmstadt
- Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie
- Technische Unitersität Darmstadt
- 64287 Darmstadt
- Germany
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30
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Schmidts V. Perspectives in the application of residual dipolar couplings in the structure elucidation of weakly aligned small molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:54-60. [PMID: 27743456 DOI: 10.1002/mrc.4543] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 05/28/2023]
Abstract
This perspective article aims to review the general methodology in the application of residual dipolar couplings (RDCs) in the structure elucidation of small molecules and give the author's view on challenges for future applications. Recent improvements in the availability of alignment media, new pulse sequences for the measurement of couplings and improvements in the analysis software have garnered widespread interest in the technique. However, further generalization is needed in order to make RDC analysis into a truly "routine" method. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
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31
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Procházková E, Kolmer A, Ilgen J, Schwab M, Kaltschnee L, Fredersdorf M, Schmidts V, Wende RC, Schreiner PR, Thiele CM. Uncovering Key Structural Features of an Enantioselective Peptide-Catalyzed Acylation Utilizing Advanced NMR Techniques. Angew Chem Int Ed Engl 2016; 55:15754-15759. [DOI: 10.1002/anie.201608559] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Eliška Procházková
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
- On leave from Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; Flemingovo nám. 2 166 10 Prague Czech Republic
| | - Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
| | - Julian Ilgen
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
| | - Mira Schwab
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
| | - Lukas Kaltschnee
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
| | - Maic Fredersdorf
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
| | - Raffael C. Wende
- Institut für Organische Chemie; Justus-Liebig-Universität; Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Peter R. Schreiner
- Institut für Organische Chemie; Justus-Liebig-Universität; Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 16 64287 Darmstadt Germany
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32
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Procházková E, Kolmer A, Ilgen J, Schwab M, Kaltschnee L, Fredersdorf M, Schmidts V, Wende RC, Schreiner PR, Thiele CM. Aufklärung entscheidender struktureller Aspekte einer enantioselektiven Peptid-katalysierten Acylierung mittels moderner NMR-Techniken. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eliška Procházková
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
- Beurlaubt vom Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; Flemingovo nám. 2 166 10 Prague Tschechische Republik
| | - Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
| | - Julian Ilgen
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
| | - Mira Schwab
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
| | - Lukas Kaltschnee
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
| | - Maic Fredersdorf
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
| | - Raffael C. Wende
- Institut für Organische Chemie; Justus-Liebig-Universität; Heinrich-Buff-Ring 17 35392 Gießen Deutschland
| | - Peter R. Schreiner
- Institut für Organische Chemie; Justus-Liebig-Universität; Heinrich-Buff-Ring 17 35392 Gießen Deutschland
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Straße 16 64287 Darmstadt Deutschland
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33
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Thiele CM, Kolmer A. Response to "Comment on "Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone" by I.A. Khodov, M.G. Kiselev, V.V. Klochkov, S.V. Efimov [http://dx.doi.org/10.1016/j.jmr.2016.02.009]" - Or Life is about compromises. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 266:69-72. [PMID: 26947752 DOI: 10.1016/j.jmr.2016.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
| | - Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
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34
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Kolmer A, Edwards LJ, Kuprov I, Thiele CM. Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 261:101-109. [PMID: 26556179 DOI: 10.1016/j.jmr.2015.10.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
To understand the properties and/or reactivity of an organic molecule, an understanding of its three-dimensional structure is necessary. Simultaneous determination of configuration and conformation often poses a daunting challenge. Thus, the more information accessible for a given molecule, the better. Additionally to (3)J-couplings, two sources of information, quantitative NOE and more recently also RDCs, are used for conformational analysis by NMR spectroscopy. In this paper, we compare these sources of conformational information in two molecules: the configurationally well-characterized strychnine 1, and the only recently configurationally and conformationally characterized α-methylene-γ-butyrolactone 2. We discuss possible sources of error in the measurement and analysis process, and how to exclude them. By this means, we are able to bolster the previously proposed flexibility for these two molecules.
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Affiliation(s)
- Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
| | - Luke J Edwards
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QG, United Kingdom
| | - Ilya Kuprov
- School of Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, University Road, Southampton SO17 1BJ, United Kingdom
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany.
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35
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Niklas T, Steinmetzger C, Liu W, Zell D, Stalke D, Ackermann L, John M. Determination of the Relative Configuration of β-Amino Acid Esters Based on Residual Dipolar Couplings. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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36
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Fredersdorf M, Göstl R, Kolmer A, Schmidts V, Monecke P, Hecht S, Thiele CM. Exploring the Conformational Space of Bridge-Substituted Dithienylcyclopentenes. Chemistry 2015; 21:14545-54. [DOI: 10.1002/chem.201501842] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 11/08/2022]
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37
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Riveira MJ, Trigo-Mouriño P, Troche-Pesqueira E, Martin GE, Navarro-Vázquez A, Mischne MP, Gil RR. Self-Sensitized Photooxygenation of 2H-Pyrans: Characterization of Unexpected Products Assisted by Computed Structural Elucidation and Residual Dipolar Couplings. J Org Chem 2015; 80:7396-402. [DOI: 10.1021/acs.joc.5b00817] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martín J. Riveira
- Instituto
de Química Rosario, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha
531, S2002LRK Rosario, Argentina
| | - Pablo Trigo-Mouriño
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Eduardo Troche-Pesqueira
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Departamento
de Química Orgánica, Edificio de Ciencias Experimentais, Universidade de Vigo,
Campus Universitario, 36310 Vigo, Spain
| | - Gary E. Martin
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065, United States
| | - Armando Navarro-Vázquez
- Departamento
de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária,
CEP 50.740-540 Recife, Pernambuco, Brazil
| | - Mirta P. Mischne
- Instituto
de Química Rosario, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha
531, S2002LRK Rosario, Argentina
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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38
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Lancefield CS, Slawin AMZ, Westwood NJ, Lebl T. The use of residual dipolar coupling for conformational analysis of structurally related natural products. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:467-75. [PMID: 25854705 DOI: 10.1002/mrc.4213] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/23/2014] [Accepted: 12/28/2014] [Indexed: 05/28/2023]
Abstract
Determining the conformational preferences of molecules in solution remains a considerable challenge. Recently, the use of residual dipolar coupling (RDC) analysis has emerged as a key method to address this. Whilst to date the majority of the applications have focused on biomolecules including proteins and DNA, the use of RDCs for studying small molecules is gaining popularity. Having said that, the method continues to develop, and here, we describe an early case study of the quantification of conformer populations in small molecules using RDC analysis. Having been inspired to study conformational preferences by unexpected differences in the NMR spectra and the reactivity of related natural products, we showed that the use of more established techniques was unsatisfactory in explaining the experimental observations. The use of RDCs provided an improved understanding that, following use of methods to quantify conformer populations using RDCs, culminated in a rationalisation of the contrasting diastereoselectivities observed in a ketone reduction reaction.
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Affiliation(s)
- Christopher S Lancefield
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, KY16 9ST, UK
| | - Alexandra M Z Slawin
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, KY16 9ST, UK
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, KY16 9ST, UK
| | - Tomas Lebl
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, KY16 9ST, UK
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39
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Olsson S, Ekonomiuk D, Sgrignani J, Cavalli A. Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings. J Am Chem Soc 2015; 137:6270-8. [PMID: 25895902 DOI: 10.1021/jacs.5b01289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are important probes in structural biology, but their analysis is often complicated by the determination of an alignment tensor or its associated assumptions. We here apply the maximum entropy principle to derive a tensor-free formalism which allows for direct, dynamic analysis of RDCs and holds the classic tensor formalism as a special case. Specifically, the framework enables us to robustly analyze data regardless of whether a clear separation of internal and overall dynamics is possible. Such a separation is often difficult in the core subjects of current structural biology, which include multidomain and intrinsically disordered proteins as well as nucleic acids. We demonstrate the method is tractable and self-consistent and generalizes to data sets comprised of observations from multiple different alignment conditions.
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Affiliation(s)
- Simon Olsson
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland.,‡Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Dariusz Ekonomiuk
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Jacopo Sgrignani
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Andrea Cavalli
- †Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland.,§Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
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40
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Zangger K. Pure shift NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:1-20. [PMID: 25919196 DOI: 10.1016/j.pnmrs.2015.02.002] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 05/08/2023]
Abstract
Although scalar-coupling provides important structural information, the resulting signal splittings significantly reduce the resolution of NMR spectra. Limited resolution is a particular problem in proton NMR experiments, resulting in part from the limited proton chemical shift range (∼10 ppm) but even more from the splittings due to scalar coupling to nearby protons. "Pure shift" NMR spectroscopy (also known as broadband homonuclear decoupling) has been developed for disentangling overlapped proton NMR spectra. The resulting spectra are considerably simplified as they consist of single lines, reminiscent of proton-decoupled C-13 spectra at natural abundance, with no multiplet structure. The different approaches to obtaining pure shift spectra are reviewed here and several applications presented. Pure shift spectra are especially useful for highly overlapped proton spectra, as found for example in reaction mixtures, natural products and biomacromolecules.
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Affiliation(s)
- Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria.
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41
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Frank AO, Freudenberger JC, Shaytan AK, Kessler H, Luy B. Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:213-217. [PMID: 25612077 DOI: 10.1002/mrc.4181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/23/2014] [Accepted: 10/11/2014] [Indexed: 06/04/2023]
Abstract
Residual dipolar couplings are highly useful NMR parameters for calculating and refining molecular structures, dynamics, and interactions. For some applications, however, it is inevitable that the preferred orientation of a molecule in an alignment medium is calculated a priori. Several methods have been developed to predict molecular orientations and residual dipolar couplings. Being beneficial for macromolecules and selected small-molecule applications, such approaches lack sufficient accuracy for a large number of organic compounds for which the fine structure and eventually the flexibility of all involved molecules have to be considered or are limited to specific, well-studied liquid crystals. We introduce a simplified model for detailed all-atom molecular dynamics calculations with a polymer strand lined up along the principal axis as a new approach to simulate the preferred orientation of small to medium-sized solutes in polymer-based, gel-type alignment media. As is shown by a first example of strychnine in a polystyrene/CDCl3 gel, the simulations potentially enable the accurate prediction of residual dipolar couplings taking into account structural details and dynamic averaging effects of both the polymer and the solute.
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Affiliation(s)
- Andreas O Frank
- Institute for Advanced Study at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany
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42
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Di Pietro ME, Aroulanda C, Merlet D, Celebre G, De Luca G. Conformational Investigation in Solution of a Fluorinated Anti-inflammatory Drug by NMR Spectroscopy in Weakly Ordering Media. J Phys Chem B 2014; 118:9007-16. [DOI: 10.1021/jp505084g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Maria Enrica Di Pietro
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, via P.
Bucci, 87036, Arcavacata
di Rende, Cosenza, Italy
- Equipe
de RMN
en milieu orienté, ICMMO, UMR 8182, Université Paris-Sud, 15 Rue Georges Clemenceau, 91405 Orsay, France
| | - Christie Aroulanda
- Equipe
de RMN
en milieu orienté, ICMMO, UMR 8182, Université Paris-Sud, 15 Rue Georges Clemenceau, 91405 Orsay, France
| | - Denis Merlet
- Equipe
de RMN
en milieu orienté, ICMMO, UMR 8182, Université Paris-Sud, 15 Rue Georges Clemenceau, 91405 Orsay, France
| | - Giorgio Celebre
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, via P.
Bucci, 87036, Arcavacata
di Rende, Cosenza, Italy
| | - Giuseppina De Luca
- Dipartimento
di Chimica e Tecnologie Chimiche, Università della Calabria, via P.
Bucci, 87036, Arcavacata
di Rende, Cosenza, Italy
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43
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Bell NGA, Rigg G, Masters S, Bella J, Uhrín D. Detecting low-level flexibility using residual dipolar couplings: a study of the conformation of cellobiose. Phys Chem Chem Phys 2014; 15:18223-34. [PMID: 24064673 DOI: 10.1039/c3cp52987h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed novel NMR methods for the measurement of heteronuclear residual dipolar couplings (RDCs) in molecules with severely overlapping NMR resonances. These and other methods enabled us to obtain 31 RDCs for α-D-cellobiose and 24 RDCs for β-D-cellobiose. The interpretation of the data in the approximation of a rigid disaccharide structure, using RDCs and interglycosidic (3)J coupling constants, yielded conformation that is very close to that determined using X-ray crystallography. However, depending on which ring was used to calculate the order parameters, the dihedral angle ψH varied up to 30° or 40°, while the φH angle was always the same. This indicates residual flexibility of the glycosidic linkage between the two monosaccharide rings and was observed for both α- and β-D-cellobiose. The RDC analysis using rigid fragments rather than a complete molecule has thus shown that the glycosidic bond of cellobiose is not completely rigid and exhibits low-level flexibility. The sources of this flexibility are discussed and evidence presented to support a hypothesis that it is associated with the ψ more than the φ angle.
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Affiliation(s)
- Nicholle G A Bell
- EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, UK.
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Trigo-Mouriño P, de la Fuente MC, Gil RR, Sánchez-Pedregal VM, Navarro-Vázquez A. Conformational Analysis of the Anti-obesity Drug Lorcaserin in Water: How To Take Advantage of Long-Range Residual Dipolar Couplings. Chemistry 2013; 19:14989-97. [DOI: 10.1002/chem.201202509] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 06/28/2013] [Indexed: 11/07/2022]
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45
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Dama M, Berger S. Ionic liquid crystals as alignment medium to measure residual dipolar couplings for carbohydrates. Carbohydr Res 2013; 377:44-7. [PMID: 23806381 DOI: 10.1016/j.carres.2013.05.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 05/23/2013] [Accepted: 05/30/2013] [Indexed: 11/19/2022]
Abstract
Ionic liquids consisting of N-dodecyl-N-methyl pyrrolidinium bromide [C12MPB] in a mixture with D2O, decanol, and DMSO were for the first time found to give anisotropic molecular alignment in magnetic fields and are useful to measure residual dipolar couplings (RDCs) from polar analytes, for example, glucose. The system shows less quadrupolar splitting of the deuterated solvent signal compared with other liquid crystal systems and hence less undesired line broadening.
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Affiliation(s)
- Murali Dama
- Institute of Analytical Chemistry, University Leipzig, Leipzig, Germany
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Schmidts V, Fredersdorf M, Lübken T, Porzel A, Arnold N, Wessjohann L, Thiele CM. RDC-based determination of the relative configuration of the fungicidal cyclopentenone 4,6-diacetylhygrophorone A12. JOURNAL OF NATURAL PRODUCTS 2013; 76:839-844. [PMID: 23659349 DOI: 10.1021/np300728b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The hygrophorones, a class of cyclopentenones isolated from fruiting bodies of the genus Hygrophorus (basidiomycetes), show promising antifungal activity. While the constitution of 4,6-diacetylhygrophorone A(12) (3) and the relative configuration of the stereogenic centers in the cyclopentenone ring were elucidated using standard NMR and MS techniques, the relative configuration of the exocyclic stereogenic center could not be assigned. By introducing a sample of 3 into an alignment medium and measuring anisotropic NMR parameters, namely, residual dipolar couplings, we were able to unambiguously determine the relative configuration of all three stereogenic centers in 4,6-diacetylhygrophorone A(12) simultaneously by fitting several structure proposals to the experimental data.
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Affiliation(s)
- Volker Schmidts
- Clemens Schöpf Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstraße 22, Darmstadt, Germany
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Giraudeau P, Montag T, Charrier B, Thiele CM. Fast access to residual dipolar couplings by single-scan 2D NMR in oriented media. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S53-S57. [PMID: 22865710 DOI: 10.1002/mrc.3856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/10/2012] [Accepted: 07/10/2012] [Indexed: 06/01/2023]
Abstract
Residual dipolar couplings (RDCs) have revolutionized the structure determination of biomolecular and organic compounds. So far, their measurement has been rather time-consuming, but one might imagine that RDCs can one day also be useful in the investigation of compounds with limited stability or short lifetimes. For such applications, it is indispensable to shorten the experiment time. In this communication, we show the first measurement of RDCs from single-scan two-dimensional NMR. An ultrafast HSQC NMR pulse sequence is presented, which includes several of the recent improvements brought to ultrafast NMR in terms of sensitivity, resolution, and spectral width. Ultrafast spectra are obtained in as little time as 60 s on an organic compound at natural abundance, namely (+)-isopinocampheol. When extracting the RDCs from these ultrafast data, a good agreement with those extracted from conventional spectra (obtained in a much longer time) is observed. These results point out the efficiency of the ultrafast approach, particularly when considering the total experiment duration.
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Affiliation(s)
- Patrick Giraudeau
- CNRS, CEISAM UMR 6230, BP 92208, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 03, France.
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Canales A, Jiménez-Barbero J, Martín-Pastor M. Review: Use of residual dipolar couplings to determine the structure of carbohydrates. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S80-S85. [PMID: 23280664 DOI: 10.1002/mrc.3888] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 09/08/2012] [Accepted: 09/20/2012] [Indexed: 05/28/2023]
Abstract
Solution nuclear magnetic resonance spectroscopy is especially useful in the carbohydrate field. The measurement of residual dipolar couplings provides long-range structural information, a valuable complement for the structural study of carbohydrates either in its free form or in the bound state to proteins. They permit to deduce the geometry and the flexibility of the glycosidic linkages, which have a major influence on the conformation of carbohydrates and their overall shape. This article reviews the current application of the residual dipolar couplings methodology to carbohydrates.
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Affiliation(s)
- A Canales
- Department Organic Chemistry, Universidad Complutense de Madrid, Madrid, Spain
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Navarro-Vázquez A. MSpin-RDC. A program for the use of residual dipolar couplings for structure elucidation of small molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S73-S79. [PMID: 23280663 DOI: 10.1002/mrc.3905] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 10/24/2012] [Accepted: 11/06/2012] [Indexed: 05/28/2023]
Abstract
We developed a new program, MSpin-RDC for the analysis of residual dipolar coupling data. This software, specially designed for small molecule analysis, can directly read many molecular-modeling and popular chemistry file formats and accept RDC values as a simple free-format table. Alignment tensor can then be computed by singular value decomposition, as well as predicted using inertia and gyration tensor-based methodologies. Trial structures are then ranked according to their Cornilescu's quality factor (Q) values. Analysis of multiconformational problems and fitting of RDC data to relative populations can be accomplished using the single-tensor approximation.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Orgánica, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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50
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Krupp A, Reggelin M. Phenylalanine-based polyarylacetylenes as enantiomer-differentiating alignment media. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S45-S52. [PMID: 23280660 DOI: 10.1002/mrc.3894] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/03/2012] [Accepted: 09/27/2012] [Indexed: 05/28/2023]
Abstract
Lyotropic liquid crystalline phases of a phenylalanine-based polyacetylene are introduced as new enantiodifferentiating alignment media. Based on the unusual temperature dependence of the quadrupolar splitting of the (2)H-signal of the solvent (CDCl(3)), three distinct states of the phase with different orientational properties can be identified. This offers the opportunity to measure multiple alignment data sets without changing the sample. Unexpectedly, the largest difference in the orientation of the enantiomers of isopinocampheol was found in the high temperature domain of the phase. This is even more astonishing because the helical structure of the polymer backbone seems to break down at temperatures above approximately 10 °C, leaving the stereogenic centers of the amino acid moieties in the repeating units as the only reason for the enantiodifferentiation.
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Affiliation(s)
- Alexis Krupp
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
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