1
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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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2
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Structures Controlled by Entropy: The Flexibility of Strychnine as Example. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227987. [PMID: 36432085 PMCID: PMC9692940 DOI: 10.3390/molecules27227987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term TΔS of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and 3JHH couplings as well.
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3
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Yu G, Wang G, Duan M, Jiang B, Zhang X, Li C, He L, Liu M. Self-Assembled Oligopeptide (FK) 4 as a Chiral Alignment Medium for the Anisotropic NMR Analysis of Organic Compounds. ACS APPLIED MATERIALS & INTERFACES 2022; 14:29223-29229. [PMID: 35712808 DOI: 10.1021/acsami.2c05506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anisotropic NMR parameters have been proven to be powerful for the structural elucidation of organic molecules. Herein, we present an alignment medium based on the self-assembled (FK)4 oligopeptide, showing excellent properties in measurements of anisotropic NMR parameters in both D2O and CD3OD. The preparation of the (FK)4-based alignment medium is simple and rapid. The low viscosity of the anisotropic phase makes it easy to be transferred to the NMR tube. The alignment of the oligopeptide is fast, stable, and homogeneous, with weak background signals, permitting the acquirement of high-quality NMR spectra. The performance of this alignment medium in residual dipolar coupling measurements and diastereomer discriminations is demonstrated by analyzing several different analytes. The enantiodiscrimination property of the (FK)4 oligopeptide is revealed by the difference of residual chemical shift anisotropy of the two enantiomers in the 1D 13C spectrum, granting its potential use for the quantification and identification of enantiomers of small molecules.
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Affiliation(s)
- Gangjin Yu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guan Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mojie Duan
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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4
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Knoll K, Herold D, Hirschmann M, Thiele CM. A supramolecular and liquid crystalline water-based alignment medium based on azobenzene-substituted 1,3,5-benzenetricarboxamides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:563-571. [PMID: 35266585 DOI: 10.1002/mrc.5266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
A supramolecular, lyotropic liquid crystalline alignment medium based on an azobenzene-containing 1,3,5-benzenetricarboxamide (BTA) building block is described and investigated. As we demonstrate, this water-based system is suitable for the investigation of various water-soluble analytes and allows for a scaling of alignment strength through variation of temperature. Additionally, alignment is shown to reversibly collapse above a certain temperature, yielding an isotropic solution. This collapse allows for isotropic reference measurements, which are typically needed in addition to those in an anisotropic environment, to be performed using the same sample just by varying the temperature. The medium described thus provides easy access to anisotropic NMR observables and simplifies structure elucidation techniques based thereon.
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Affiliation(s)
- Kevin Knoll
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Dominik Herold
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Max Hirschmann
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christina M Thiele
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
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5
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Salvino RA, De Luca G, Celebre G. Assessing the chirality-dependent conformational distribution of small flexible opposite enantiomers dissolved in weakly ordering enantiopure media by means of liquid crystal NMR techniques. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Knoll K, Kostner T, Lorenz C, Thiele C. Investigations into Supramolecular Lyotropic Liquid Crystals based on 1,3,5‐Benzenetricarboxaramides by NMR‐spectroscopy. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kevin Knoll
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry GERMANY
| | - Tobias Kostner
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry GERMANY
| | - Christian Lorenz
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry GERMANY
| | - Christina Thiele
- Technische Universität Darmstadt: Technische Universitat Darmstadt Chemistry Alarich Weiss Strasse 16 64287 Darmstadt GERMANY
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7
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Li GW, Wang XJ, Lei X, Liu N, Wu ZQ. Self-assembly of Helical Polymers and Oligomers to Create Liquid Crystalline Alignment for Anisotropic NMR Parameters. Macromol Rapid Commun 2022; 43:e2100898. [PMID: 35076973 DOI: 10.1002/marc.202100898] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/22/2022] [Indexed: 11/07/2022]
Abstract
The measurement of anisotropic residual dipolar couplings (RDCs) parameters for the structure elucidation of organic molecules relies on suitable alignment media. Employment of self-assembled liquid crystalline systems to create anisotropic alignment can be an effective way to realize aligned samples and acquire RDCs. This Mini-review highlights the recent advances on amino acid-based helical polymers and supramolecular oligomers forming rigid, rod-like structures that aggregate into ordered liquid crystalline phases, including amino acid-based helical polyisocyanides, polyacetylenes, polypeptides, and oligopeptides assembled alignment media. The methodology for the determination of anisotropic liquid crystals was briefly discussed, and a summary of recent research progress in the enantiodifferentiation of helical polymers aligned media was followed. In addition, the self-assembled mechanism of oligopeptides and their RDCs structural analysis were also described. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gao-Wei Li
- College of Chemistry and Chemical Engineering, and Henan Engineering Laboratory of Green Synthesis for Pharmaceuticals, Shangqiu Normal University, Shangqiu, Henan Province, 476000, China
| | - Xiao-Juan Wang
- College of Chemistry and Chemical Engineering, and Henan Engineering Laboratory of Green Synthesis for Pharmaceuticals, Shangqiu Normal University, Shangqiu, Henan Province, 476000, China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, P. R. China
| | - Na Liu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, and Anhui Key Laboratory of Advanced Functional Materials and Devices, Hefei University of Technology, Hefei, Anhui Province, 230009, China
| | - Zong-Quan Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin Province, 130012, China
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8
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Wesp S, Wolf K, Immel S, Reggelin M. Poly(arylisocyanides) as Versatile, Enantiodiscriminating Alignment Media for Small Molecules. Chempluschem 2022; 87:e202100507. [PMID: 35072980 DOI: 10.1002/cplu.202100507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/02/2022] [Indexed: 11/08/2022]
Abstract
Lyotropic liquid crystalline (LLC) phases of amino acid derived polyarylisocyanides were employed as chiral alignment media for the measurement of residual dipolar couplings (RDCs) of small chiral organic molecules. Anisotropic samples in CDCl3 displayed quadrupolar splittings of the deuterium signal in the range of several hundreds of Hertz. The LLC phases showed excellent orienting properties for a broad range of analytes bearing various functional groups. The precise extraction of RDCs in the range of up to ±40 Hertz from F2-coupled HSQC spectra was possible. Additionally, the chiral environment offers the opportunity for diastereomorphous interactions with the enantiomers of chiral analytes leading to two different sets of RDCs. This differential order effect was particularly pronounced with ketones and alcohols.
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Affiliation(s)
- Svenja Wesp
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Kai Wolf
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Stefan Immel
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Michael Reggelin
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
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9
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Aroulanda C, Lesot P. Molecular enantiodiscrimination by NMR spectroscopy in chiral oriented systems: Concept, tools, and applications. Chirality 2021; 34:182-244. [PMID: 34936130 DOI: 10.1002/chir.23386] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
The study of enantiodiscriminations in relation to various facets of enantiomorphism (chirality/prochirality) and/or molecular symmetry is an exciting area of modern organic chemistry and an ongoing challenge for nuclear magnetic resonance (NMR) spectroscopists who have developed many useful analytical approaches to solve stereochemical problems. Among them, the anisotropic NMR using chiral aligning solvents has provided a set of new and original tools by making accessible all intramolecular, order-dependent NMR interactions (anisotropic interactions), such as residual chemical shift anisotropy (RCSA), residual dipolar coupling (RDC), and residual quadrupolar coupling (RQC) for spin I > 1/2, while preserving high spectral resolution. The force of NMR in enantiopure, oriented solvents lies on its ability to orient differently in average on the NMR timescale enantiomers of chiral molecules and enantiotopic elements of prochiral ones, leading distinct NMR spectra or signals to be detected. In this compendium mainly written for all chemists playing with (pro)chirality, we overview various key aspects of NMR in weakly aligning chiral solvents as the lyotropic liquid crystals (LLCs), in particular those developed in France to study (pro)chiral compounds in relation with chemists needs: study of enantiopurity of mixture, stereochemistry, natural isotopic fractionation, as well as molecular conformation and configuration. Key representative examples covering the diversity of enantiomorphism concept, and the main and most recent applications illustrating the analytical potential of this NMR in polypeptide-based chiral liquid crystals (CLCs) are examined. The latest analytical strategy developed to determine in-solution conformational distribution of flexibles solutes using NMR in polypeptide-based aligned solvents is also proposed.
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Affiliation(s)
- Christie Aroulanda
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
| | - Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
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10
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil-Silva LF, Gil RR. Cross-Linked Poly-4-Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021; 60:26314-26319. [PMID: 34609778 DOI: 10.1002/anie.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/07/2022]
Abstract
Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross-linked poly-4-acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) and J-coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α-helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure-based drug design.
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Affiliation(s)
- Kathleen A Farley
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Martin R M Koos
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Ye Che
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Reto Horst
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Chris Limberakis
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Justin Bellenger
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Ricardo Lira
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | | | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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11
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil‐Silva LF, Gil RR. Cross‐Linked Poly‐4‐Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
| | - Ye Che
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Reto Horst
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Chris Limberakis
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Justin Bellenger
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Ricardo Lira
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
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12
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Pedersen KD, Zhang J, Gotfredsen CH. Practical considerations for working with graphene oxide as alignment media for RDC measurements. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:738-745. [PMID: 33656175 DOI: 10.1002/mrc.5143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Katja D Pedersen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jingdong Zhang
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
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13
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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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14
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Ibáñez de Opakua A, Zweckstetter M. Extending the applicability of P3D for structure determination of small molecules. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:105-116. [PMID: 37904779 PMCID: PMC10539764 DOI: 10.5194/mr-2-105-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/15/2021] [Indexed: 11/01/2023]
Abstract
The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(γ -benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.
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Affiliation(s)
- Alain Ibáñez de Opakua
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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15
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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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16
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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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17
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Liu H, Chen P, Li XL, Sun H, Lei X. Practical aspects of oligopeptide AAKLVFF as an alignment medium for the measurements of residual dipolar coupling of organic molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:404-410. [PMID: 32239576 DOI: 10.1002/mrc.4825] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/03/2018] [Accepted: 12/26/2018] [Indexed: 06/11/2023]
Abstract
Practical aspects of the oligopeptide AAKLVFF as an alignment medium are discussed, including large-scale synthesis of the oligopeptide, detailed description of preparation of the alignment medium, and acquisition of the RDCs. The resulting orienting medium is stable and highly homogeneous with tunable alignment strength in methanol.
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Affiliation(s)
- Han Liu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, China
| | - Pian Chen
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, China
| | - Xiao-Lu Li
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Han Sun
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, China
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18
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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Determination of Complex Small-Molecule Structures Using Molecular Alignment Simulation. Angew Chem Int Ed Engl 2020; 59:6172-6176. [PMID: 31971323 PMCID: PMC7187346 DOI: 10.1002/anie.202000311] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/23/2020] [Indexed: 11/12/2022]
Abstract
Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy-based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule-specific anisotropic NMR parameters. The quantitative correlation uses an accurate three-dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ-benzyl-l-glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.
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Affiliation(s)
- Alain Ibáñez de Opakua
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
| | - Frederik Klama
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGA30602USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry and BiochemistrySeton Hall UniversitySouth OrangeNJ07079USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry & BiochemistryUniversity of North Carolina WilmingtonWilmingtonNC28409USA
| | - Markus Zweckstetter
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
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19
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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Bestimmung komplexer kleiner Molekülstrukturen mittels molekularer Ausrichtungssimulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alain Ibáñez de Opakua
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
| | - Frederik Klama
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Complex Carbohydrate Research CenterUniversity of Georgia Athens GA 30602 USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry and BiochemistrySeton Hall University South Orange NJ 07079 USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry & BiochemistryUniversity of North Carolina Wilmington Wilmington NC 28409 USA
| | - Markus Zweckstetter
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
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20
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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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21
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Ma ZK, Han XY, Liu H, Ji JC, Qin SY, Li XD, Lei X. Lyotropic liquid crystal to measure residual dipolar couplings in dimethyl sulfoxide based on modified cellulose nanocrystals. NEW J CHEM 2020. [DOI: 10.1039/c9nj06031f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel lyotropic liquid crystal was developed for the measurement of RDCs of organic molecules with no background signals.
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Affiliation(s)
- Zong-Kai Ma
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xiao-Yang Han
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
| | - Han Liu
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
| | - Jia-Cheng Ji
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
| | - Si-Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xiang-Dan Li
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
- P. R. China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences
- South-Central University for Nationalities
- Wuhan
- P. R. China
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22
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Slavík P, Krupička M, Eigner V, Vrzal L, Dvořáková H, Lhoták P. Rearrangement of meta-Bridged Calix[4]arenes Promoted by Internal Strain. J Org Chem 2019; 84:4229-4235. [PMID: 30868881 DOI: 10.1021/acs.joc.9b00107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The meta-bridged calixarenes possess a rigidified and highly distorted cavity, where the additional single-bond bridge imposes an extreme internal strain on the whole system. As a consequence, these compounds exhibit a reasonably amended reactivity, compared with common calix[4]arene derivatives, which is governed by the release of internal strain. This can be documented by the reaction of the bridged calix[4]arene with P2O5 or Nafion-H, leading (apart from polymers) to a macrocyclic product with a rearranged basic skeleton. The methylene bridge next to the fluorene moiety is intramolecularly shifted from position 2 to position 4 of the phenolic subunit to minimize the tension. As revealed by single-crystal X-ray analysis and by application of the residual dipolar coupling method, the rearrangement occurs without altering the original conformation.
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Affiliation(s)
- Petr Slavík
- Department of Organic Chemistry , University of Chemistry and Technology, Prague (UCTP) , Technická 5 , 166 28 Prague 6 , Czech Republic
| | - Martin Krupička
- Department of Organic Chemistry , University of Chemistry and Technology, Prague (UCTP) , Technická 5 , 166 28 Prague 6 , Czech Republic
| | - Václav Eigner
- Laboratory of Nuclear Magnetic Resonance (NMR) Spectroscopy , UCTP , 166 28 Prague 6 , Czech Republic
| | - Lukáš Vrzal
- Institute of Physics AS CR, v.v.i. , Na Slovance 2 , 182 21 Prague 8 , Czech Republic
| | - Hana Dvořáková
- Institute of Physics AS CR, v.v.i. , Na Slovance 2 , 182 21 Prague 8 , Czech Republic
| | - Pavel Lhoták
- Department of Organic Chemistry , University of Chemistry and Technology, Prague (UCTP) , Technická 5 , 166 28 Prague 6 , Czech Republic
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23
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Jeziorowski S, Thiele CM. Poly‐γ‐
p
‐Biphenylmethyl‐Glutamate as Enantiodifferentiating Alignment Medium for NMR Spectroscopy with Temperature‐Tunable Properties. Chemistry 2018; 24:15631-15637. [DOI: 10.1002/chem.201802921] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sharon Jeziorowski
- 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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24
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Li GW, Liu H, Qiu F, Wang XJ, Lei XX. Residual Dipolar Couplings in Structure Determination of Natural Products. NATURAL PRODUCTS AND BIOPROSPECTING 2018; 8:279-295. [PMID: 29943349 PMCID: PMC6102172 DOI: 10.1007/s13659-018-0174-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/14/2018] [Indexed: 05/16/2023]
Abstract
The determination of natural products stereochemistry remains a formidable task. Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for determination of the stereochemistry of organic molecule in solution. This review will provide a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized. This review provides a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized.
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Affiliation(s)
- Gao-Wei Li
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Han Liu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Feng Qiu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Xiao-Juan Wang
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Xin-Xiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China.
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25
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Determination of the conformational states of strychnine in solution using NMR residual dipolar couplings in a tensor-free approach. Methods 2018; 148:4-8. [PMID: 30036639 DOI: 10.1016/j.ymeth.2018.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 12/14/2022] Open
Abstract
Small molecules with rotatable bonds can occupy different conformational states in solution as a consequence of their thermal fluctuations. The accurate determination of the structures of such states, as well as of their statistical weights, has been challenging because of the technical difficulties in extracting information from experimental measurements, which are normally averaged over the conformational space available. Here, to achieve this objective, we present an approach based on a recently proposed tensor-free method for incorporating NMR residual dipolar couplings as structural restraints in replica-averaged molecular dynamics simulations. This approach enables the information provided by the experimental data to be used in the spirit of the maximum entropy principle to determine the structural ensembles of small molecules. Furthermore, in order to enhance the sampling of the conformational space we incorporated the metadynamics method in the simulations. We illustrate the method in the case of strychnine, determining the three major conformational states of this small molecule and their associated occupation probabilities.
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26
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Landovský T, Tichotová M, Vrzal L, Budka J, Eigner V, Dvořáková H, Lhoták P. Structure elucidation of phenoxathiin-based thiacalix[4]arene conformations using NOE and RDC data. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Navarro-Vázquez A, Gil RR, Blinov K. Computer-Assisted 3D Structure Elucidation (CASE-3D) of Natural Products Combining Isotropic and Anisotropic NMR Parameters. JOURNAL OF NATURAL PRODUCTS 2018; 81:203-210. [PMID: 29323895 DOI: 10.1021/acs.jnatprod.7b00926] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A computer-assisted structural elucidation (CASE-3D) strategy based on the use of isotropic and/or anisotropic NMR data is proposed to elucidate relative configuration and preferred conformation in complex natural products. The methodology involves the selection of conformational models through the use of the Akaike Information Criterion and scoring of the different configurations. As illustrative examples, the methodology furnished the correct configuration of the already known compounds artemisinin (1) and homodimericin A (2). Revised structures (5 and 6), including their absolute configuration, for the recently reported curcusones I (3) and J (4) are proposed.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco , Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Kirill Blinov
- MestReLab Research S. L. Feliciano Barrera , 9 Baixo, Santiago de Compostela, A Coruña, 15706 Spain
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28
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Marcó N, Nolis P, Gil RR, Parella T. 2J HH-resolved HSQC: Exclusive determination of geminal proton-proton coupling constants. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 282:18-26. [PMID: 28686954 DOI: 10.1016/j.jmr.2017.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 06/07/2023]
Abstract
The measurement of two-bond proton-proton coupling constants (2JHH) in prochiral CH2 groups from the F2 dimension of 2D spectra is not easy due to the usual presence of complex multiplet J patterns, line broadening effects and strong coupling artifacts. These drawbacks are particularly pronounced and frequent in AB spin systems, as those normally exhibited by the pair of diastereotopic CH2 protons. Here, a novel 2JHH-resolved HSQC experiment for the exclusive and accurate determination of the magnitude of 2JHH from the doublet displayed along the highly-resolved indirect F1 dimension is described. A pragmatic 2JHH NMR profile affords a fast overview of the full range of existing 2JHH values. In addition, a 2JHH/δ(13C)-scaled version proves to be an efficient solution when severe signal overlapping complicate a rigorous analysis. The performance of the method is compared with other current techniques and illustrated by the determination of challenging residual dipolar 2DHH coupling constants of small molecules dissolved in weakly orienting media.
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Affiliation(s)
- Núria Marcó
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Catalonia, Spain.
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29
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Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules. ACS Chem Biol 2017; 12:2157-2163. [PMID: 28617580 DOI: 10.1021/acschembio.7b00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.
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Affiliation(s)
| | - René F. Ramos Alvarenga
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Thomas P. Wyche
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biological
Chemistry and Molecular Pharmacology Department, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | | | | | | | - Charles D. Schwieters
- Center for
Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, United States
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30
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Reller M, Wesp S, Koos MRM, Reggelin M, Luy B. Biphasic Liquid Crystal and the Simultaneous Measurement of Isotropic and Anisotropic Parameters by Spatially Resolved NMR Spectroscopy. Chemistry 2017. [DOI: 10.1002/chem.201702126] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Malin Reller
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Svenja Wesp
- Organische Chemie; Technische Universität Darmstadt; Alarich-Weiss Str. 4 64287 Darmstadt Germany
| | - Martin R. M. Koos
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Michael Reggelin
- Organische Chemie; Technische Universität Darmstadt; Alarich-Weiss Str. 4 64287 Darmstadt Germany
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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31
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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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32
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Marcó N, Gil RR, Parella T. Structural discrimination from in situ measurement of 1 D CH and 2 D HH residual dipolar coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:540-545. [PMID: 28043096 DOI: 10.1002/mrc.4575] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
A fast residual dipolar coupling constant-assisted strategy involving the simultaneous determination of scalar and total coupling constants from a single 1 JCH /2 JHH -resolved NMR spectrum is reported. It is shown that the concerted use of the directly measured 1 DCH (for all CHn multiplicities) and 2 DHH residual dipolar couplings allows an on-the-fly assignment of diastereotopic CH2 protons, as well as of an efficient discrimination between diastereoisomeric structures of strychnine which contains six stereocenters. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Núria Marcó
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
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33
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Navarro-Vázquez A, Berdagué P, Lesot P. Integrated Computational Protocol for the Analysis of Quadrupolar Splittings from Natural-Abundance Deuterium NMR Spectra in (Chiral) Oriented Media. Chemphyschem 2017; 18:1252-1266. [DOI: 10.1002/cphc.201601423] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental; Universidade Federal de Pernambuco Cidade Universitária; CEP: 50 740-540 Recife PE Brazil
- Institute of Organic Chemistry and Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe German
| | - Philippe Berdagué
- RMN en Milieu Orienté; ICMMO; UMR CNRS 8182; Université Paris-Sud/Université Paris-Saclay; Bât. 410 91405 Orsay cedex France
| | - Philippe Lesot
- RMN en Milieu Orienté; ICMMO; UMR CNRS 8182; Université Paris-Sud/Université Paris-Saclay; Bât. 410 91405 Orsay cedex France
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34
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García ME, Woodruff SR, Hellemann E, Tsarevsky NV, Gil RR. Di(ethylene glycol) methyl ether methacrylate (DEGMEMA)-derived gels align small organic molecules in methanol. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:206-209. [PMID: 26763068 DOI: 10.1002/mrc.4400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 10/20/2015] [Accepted: 11/24/2015] [Indexed: 05/28/2023]
Abstract
Residual dipolar couplings (RDCs) constitute an important NMR parameter for structural elucidation in all areas of chemistry. In this study, di(ethylene glycol) methyl ether methacrylate (DEGMEMA)-based gels are introduced as alignment media for the measurement of RDCs of small organic molecules in polar solvents such as methanol. The low viscosity of methanol permits the execution of J-scaled BIRD HSQC experiments that yield very sharp lines in anisotropic conditions. The gels have excellent mechanical properties, and their compression and expansion in the swollen state can be reversed and performed multiple times. This process enables the easy loading and release of analytes. The excellent performance of these new aligning gels is demonstrated by analyzing the structure of the alkaloid retrorsine. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Manuela E García
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
- Department of Organic Chemistry, National University of Cordoba, Medina Allende y Haya de La Torre, Cordoba, 5000, Argentina
| | - Shannon R Woodruff
- Department of Chemistry, Southern Methodist University, Dallas, TX, USA
- Center for Drug Discovery, Design, and Delivery in Dedman College, Southern Methodist University, Dallas, TX, USA
| | - Erich Hellemann
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Nicolay V Tsarevsky
- Department of Chemistry, Southern Methodist University, Dallas, TX, USA
- Center for Drug Discovery, Design, and Delivery in Dedman College, Southern Methodist University, Dallas, TX, USA
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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35
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Marcó N, Souza AA, Nolis P, Gil RR, Parella T. Perfect 1J CH-resolved HSQC: Efficient measurement of one-bond proton-carbon coupling constants along the indirect dimension. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 276:37-42. [PMID: 28092787 DOI: 10.1016/j.jmr.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/30/2016] [Accepted: 01/01/2017] [Indexed: 06/06/2023]
Abstract
A versatile 1JCH-resolved HSQC pulse scheme for the speedy, accurate and automated determination of one-bond proton-carbon coupling constants is reported. The implementation of a perfectBIRD element allows a straightforward measurement from the clean doublets obtained along the highly resolved F1 dimension, even for each individual 1JCHa and 1JCHb in diastereotopic HaCHb methylene groups. Real-time homodecoupling during acquisition and other alternatives to minimize accidental signal overlapping in overcrowded spectra are also discussed.
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Affiliation(s)
- N Marcó
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
| | - A A Souza
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain; Departamento de Química, Universidade Federal do Piauí, 64049-550 Teresina, PI, Brazil
| | - P Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
| | - R R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - T Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain.
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36
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Marcó N, Souza AA, Nolis P, Cobas C, Gil RR, Parella T. 1JCH NMR Profile: Identification of Key Structural Features and Functionalities by Visual Observation and Direct Measurement of One-Bond Proton-Carbon Coupling Constants. J Org Chem 2017; 82:2040-2044. [DOI: 10.1021/acs.joc.6b02873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Núria Marcó
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
| | - Alexandre A. Souza
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
- Departamento
de Química, Universidade Federal do Piauí, Teresina, PI 64049-550, Brazil
| | - Pau Nolis
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
| | - Carlos Cobas
- Mestrelab Research, Santiago de Compostela, E-15706 A Coruña, Spain
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Teodor Parella
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
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37
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Šoral M, Markus J, Doháňošová J, Šoralová S, Dvoranová D, Chyba A, Moncol J, Berkeš D, Liptaj T. An unexpected reaction pathway in the synthesis of the ABCE framework of strychnine-type alkaloids – A multidisciplinary study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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Hellemann E, Teles RR, Hallwass F, Barros W, Navarro-Vázquez A, Gil RR. Mechanical Behavior of Polymer Gels for RDCs and RCSAs Collection: NMR Imaging Study of Buckling Phenomena. Chemistry 2016; 22:16632-16635. [DOI: 10.1002/chem.201603333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Erich Hellemann
- Department of Chemistry; Carnegie Mellon University; 4400 Fifth Ave. Pittsburgh PA 15213 USA
| | - Rubens R. Teles
- Departamento de Química Fundamental; Universidade Federal de Pernambuco; Cidade Universitária CEP,50.740-540 Recife, PE Brazil
| | - Fernando Hallwass
- Departamento de Química Fundamental; Universidade Federal de Pernambuco; Cidade Universitária CEP,50.740-540 Recife, PE Brazil
| | - W. Barros
- Departamento de Física; Universidade Federal de Pernambuco; Cidade Universitária CEP,50.740-540 Recife, PE Brazil
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental; Universidade Federal de Pernambuco; Cidade Universitária CEP,50.740-540 Recife, PE Brazil
| | - Roberto R. Gil
- Department of Chemistry; Carnegie Mellon University; 4400 Fifth Ave. Pittsburgh PA 15213 USA
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39
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Hansmann S, Larem née Montag T, Thiele CM. Enantiodifferentiating Properties of the Alignment Media PELG and PBLG - A Comparison. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501410] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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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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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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Castañar L, Sistaré E, Virgili A, Williamson RT, Parella T. Suppression of phase and amplitude J(HH) modulations in HSQC experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:115-119. [PMID: 25279825 DOI: 10.1002/mrc.4149] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/11/2014] [Accepted: 08/25/2014] [Indexed: 06/03/2023]
Abstract
The amplitude and the phase of cross peaks in conventional 2D HSQC experiments are modulated by both proton-proton, J(HH), and proton-carbon, (1)J(CH), coupling constants. It is shown by spectral simulation and experimentally that J(HH) interferences are suppressed in a novel perfect-HSQC pulse scheme that incorporates perfect-echo INEPT periods. The improved 2D spectra afford pure in-phase cross peaks with respect to (1)J(CH) and J(HH), irrespective of the experiment delay optimization. In addition, peak volumes are not attenuated by the influence of J(HH), rendering practical issues such as phase correction, multiplet analysis, and signal integration more appropriate.
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Affiliation(s)
- Laura Castañar
- Servei de Ressonància Magnètica Nuclear, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Catalonia, Spain; Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Catalonia, Spain
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43
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Vrzal L, Kratochvílová-Šimánová M, Landovský T, Polívková K, Budka J, Dvořáková H, Lhoták P. Application of RDC enhanced NMR spectroscopy in structural analysis of thiacalix[4]arene derivatives. Org Biomol Chem 2015; 13:9610-8. [DOI: 10.1039/c5ob01424g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The conformational behaviour of novel phenoxathiin-based skeletons was studied using the Residual Dipolar Coupling constant (RDC) method.
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Affiliation(s)
- L. Vrzal
- Laboratory of NMR Spectroscopy
- University of Chemistry and Technology
- 166 28 Prague 6
- Czech Republic
| | | | - T. Landovský
- Department of Organic Chemistry
- University of Chemistry and Technology
- 166 28 Prague 6
- Czech Republic
| | - K. Polívková
- Department of Organic Chemistry
- University of Chemistry and Technology
- 166 28 Prague 6
- Czech Republic
| | - J. Budka
- Department of Organic Chemistry
- University of Chemistry and Technology
- 166 28 Prague 6
- Czech Republic
| | - H. Dvořáková
- Laboratory of NMR Spectroscopy
- University of Chemistry and Technology
- 166 28 Prague 6
- Czech Republic
| | - P. Lhoták
- Department of Organic Chemistry
- University of Chemistry and Technology
- 166 28 Prague 6
- Czech Republic
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44
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Lesot P, Aroulanda C, Zimmermann H, Luz Z. Enantiotopic discrimination in the NMR spectrum of prochiral solutes in chiral liquid crystals. Chem Soc Rev 2015; 44:2330-75. [DOI: 10.1039/c4cs00260a] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theory and applications to stereo- and bio-chemistry of the discrimination of enantiotopic elements observed in the NMR spectra of prochiral solutes dissolved in chiral liquid crystals are comprehensively discussed.
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Affiliation(s)
- Philippe Lesot
- Laboratoire de RMN en Milieu Orienté CNRS UMR 8182
- ICMMO
- 91405 Orsay cedex
- France
| | - Christie Aroulanda
- Laboratoire de RMN en Milieu Orienté CNRS UMR 8182
- ICMMO
- 91405 Orsay cedex
- France
| | - Herbert Zimmermann
- Abteilung Biophysik
- Max-Planck-Institut für Medizinische Forschung
- 69120 Heidelberg
- Germany
| | - Zeev Luz
- Weizmann Institute of Science
- Department of Chemical Physics
- Rehovot 76100
- Israel
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45
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Saurí J, Castañar L, Nolis P, Virgili A, Parella T. Straightforward measurement of individual (1)J(CH) and (2)J(HH) in diastereotopic CH(2) groups. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 242:33-40. [PMID: 24602927 DOI: 10.1016/j.jmr.2014.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/31/2014] [Accepted: 02/02/2014] [Indexed: 06/03/2023]
Abstract
The C-H(A) cross-peak corresponding to a diastereotopic CHAHB methylene spin system exhibits a characteristic 1:0:1 multiplet pattern along the indirect dimension of a ω1-coupled HSQC spectrum. It is shown here that the use of the initial (13)C Boltzmann polarization instead of the regular INEPT-based (1)H Boltzmann polarization makes visible the central lines of this multiplet pattern. A spin-state-selective method is proposed for the efficient measurement of both (1)J(CHA) and (1)J(CHB) along the indirect dimension of a 2D spectrum as well as to the magnitude and the sign of the geminal (2)J(HAHB) coupling constant from the straightforward analysis of a single four-component E.COSY cross-peak. Additionally, the extraction of (1)J(CH) values for CH and CH3 multiplicities can be also performed from the same spectrum. The success of the method is also illustrated for the determination of residual dipolar (1)D(CH) and (2)D(HH) coupling constants in a small molecule weakly aligned in a PMMA swollen gel.
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Affiliation(s)
- Josep Saurí
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Laura Castañar
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Pau Nolis
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Albert Virgili
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain.
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46
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Reinsperger T, Luy B. Homonuclear BIRD-decoupled spectra for measuring one-bond couplings with highest resolution: CLIP/CLAP-RESET and constant-time-CLIP/CLAP-RESET. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 239:110-120. [PMID: 24365099 DOI: 10.1016/j.jmr.2013.11.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/22/2013] [Accepted: 11/23/2013] [Indexed: 06/03/2023]
Abstract
Heteronuclear one-bond couplings are of interest for various aspects of structural analysis of small organic molecules, including for example the distinction of axial and equatorial protons or the use of RDCs as angular constraints. Such couplings are most easily measured from pure doublets in HSQC-type spectra. Recently, the fully decoupled RESET HSQC experiment was reported and several other so-called pure-shift methods followed that allow for the removal of splittings due to homonuclear scalar interactions in one and two-dimensional NMR. In this work we present broadband homonuclear decoupled CLIP/CLAP-RESET experiments based on an isotope-selective BIRD filter element using a recently reported improved version of Zangger-Sterk data chunking. The concatenated FIDs result in multiplets in which most homonuclear splittings are removed while the heteronuclear one-bond couplings are retained. Couplings can be extracted in an IPAP fashion without scaling of subspectra by the use of optimized coherence transfer elements like the COB-INEPT. The method leads to complete homonuclear decoupling for CH groups and CH3 groups in isotropic samples, but leaves residual splittings with antiphase contributions for e.g. CH2 groups due to (2)JHH coupling evolution that is not affected by the BIRD element. For this case we present a constant-time version of the proposed BIRD decoupling scheme with full homonuclear decoupling. In addition, the effects of strong coupling are discussed. Strong coupling artifacts cannot be circumvented, but the proposed experiments allow their distinct recognition.
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Affiliation(s)
- Tony Reinsperger
- Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Postfach 3640, 76021 Karlsruhe, Germany; Institut für Organische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Burkhard Luy
- Institut für Biologische Grenzflächen, Karlsruher Institut für Technologie (KIT), Postfach 3640, 76021 Karlsruhe, Germany; Institut für Organische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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47
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Merle C, Kummerlöwe G, Freudenberger JC, Halbach F, Stöwer W, Gostomski CLV, Höpfner J, Beskers T, Wilhelm M, Luy B. Crosslinked Poly(ethylene oxide) as a Versatile Alignment Medium for the Measurement of Residual Anisotropic NMR Parameters. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301929] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Merle C, Kummerlöwe G, Freudenberger JC, Halbach F, Stöwer W, Gostomski CLV, Höpfner J, Beskers T, Wilhelm M, Luy B. Crosslinked Poly(ethylene oxide) as a Versatile Alignment Medium for the Measurement of Residual Anisotropic NMR Parameters. Angew Chem Int Ed Engl 2013; 52:10309-12. [DOI: 10.1002/anie.201301929] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 06/26/2013] [Indexed: 11/07/2022]
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Parella T, Espinosa JF. Long-range proton-carbon coupling constants: NMR methods and applications. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 73:17-55. [PMID: 23962883 DOI: 10.1016/j.pnmrs.2013.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 06/02/2023]
Abstract
A general review of novel NMR methods to measure heteronuclear long-range proton-carbon coupling constants ((n)JCH; n>1) in small molecules is made. NMR experiments are classified in terms of NMR pulse scheme and cross-peak nature. A discussion about simplicity, general applicability and accuracy for each particular NMR experiment is presented and exemplified. Important aspects such as the sign determination and measurement of very small coupling values involving protonated and non-protonated carbons as well as the complementarity between different experiments are also discussed. Finally, a compilation of applications in structural and conformational analysis of different types of molecules since 2000 is surveyed.
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Affiliation(s)
- Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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Metaxas AE, Cort JR. Counterion influence on chemical shifts in strychnine salts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:292-298. [PMID: 23495106 DOI: 10.1002/mrc.3945] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/04/2013] [Accepted: 02/05/2013] [Indexed: 06/01/2023]
Abstract
The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here, we characterize the relative influence of different counterions on (1)H and (13)C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD), and chloroform-d (CDCl3) solvents. In organic solvents but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. Slight concentration dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared with the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts.
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Affiliation(s)
- Athena E Metaxas
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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