1
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Sager E, Tzvetkova P, Lingel A, Gossert AD, Luy B. Hydrogen bond formation may enhance RDC-based discrimination of enantiomers. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:639-647. [PMID: 38785031 DOI: 10.1002/mrc.5448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024]
Abstract
The distinction of enantiomers based on residual anisotropic parameters obtained by alignment in chiral poly-γ-benzyl-L-glutamate (PBLG) is among the strongest in high-resolution NMR spectroscopy. However, large variations in enantiodifferentiation among different solutes are frequently observed. One hypothesis is that the formation of hydrogen bonds between solute and PBLG is important for the distinction of enantiomers. With a small set of three almost spherical enantiomeric pairs, for which 1DCH residual dipolar couplings are measured, we address this issue in a systematic way: borneol contains a single functional group that can act as a hydrogen bond donor, camphor has a single group that may act as a hydrogen bond acceptor, and quinuclidinol can act as both hydrogen bond donor and acceptor. The results are unambiguous: although camphor shows low enantiodifferentiation with PBLG and alignment that can be predicted well by the purely steric TRAMITE approach, the distinction of enantiomers for the other enantiomeric pairs is significantly higher with alignment properties that must involve a specific interaction in addition to steric alignment.
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Affiliation(s)
- Emine Sager
- Institute of Organic Chemistry and Institute for Biological Interfaces 4-Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Novartis Biomedical Research, Basel, Switzerland
| | - Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4-Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | | | | | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4-Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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2
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Sternberg U, Tichotová MC, Tučková L, Ešnerová A, Hanus J, Baszczyňski O, Procházková E. Extending molecular dynamics with dipolar NMR tensors as constraints to chiral phosphorus compounds. Phys Chem Chem Phys 2024; 26:20814-20819. [PMID: 39044477 DOI: 10.1039/d4cp02401j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Molecular dynamics with orientational constraints (MDOC) simulations use NMR parameters as tensorial constraints in the stereochemical analysis of small molecules. 13C-31P Residual dipolar couplings-aided MDOC simulations of small phosphorus molecules determined the relative configurations of rigid molecules after including 3JH-H-couplings as additional constraints. However, flexible molecules remain a problem.
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Affiliation(s)
- Ulrich Sternberg
- COSMOS-Software, 07743 Jena, Germany
- Karlsruhe Institute of Technology (KIT), Postfach 3640, D-76021 Karlsruhe, Germany
| | - Markéta Christou Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
| | - Aneta Ešnerová
- Department of Organic Chemistry, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Jan Hanus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
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3
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Elsing D, Luy B, Kozlowska M. Enantiomer Differentiation by Interaction-Specific Prediction of Residual Dipolar Couplings in Spherical-like Molecules. J Chem Theory Comput 2024. [PMID: 39099221 DOI: 10.1021/acs.jctc.4c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Residual Dipolar Couplings (RDCs) are averaged dipolar couplings between nuclear spins of atoms in a molecule that can be measured by nuclear magnetic resonance (NMR) spectroscopy upon partial alignment by a chiral alignment medium. The estimation of differences in alignment of enantiomers may, in principle, enable the determination of absolute configuration. Here, we use molecular dynamics (MD) simulations to mimic the alignment of chiral molecules (i.e., isopinocampheol, quinuclidin-3-ol, borneol, and camphor) to the chiral poly-γ-benzyl-L-glutamate (PBLG) polymer to predict RDCs in silico and compare calculated and experimentally measured residual dipolar couplings for the four enantiomeric pairs. The aim is to validate the computational scheme for the prediction of RDCs in chiral molecules and understand the interaction leading to the alignment in more detail. We determine the indispensable importance of hydrogen bonds between a chiral molecule and the alignment medium on the overall quality of the simulated alignment and interaction poses toward high agreement with experiments. A good correlation with experimental data is found for camphor and isopinocampheol, while the correlation for quinuclidin-3-ol and borneol is lower. We attribute this observation to the high difficulty of the RDC prediction for rather almost spherical molecules. The study reveals that the prediction of alignment with small enantiomeric differences is possible with an MD-based approach; however, extended simulation times (e.g., 50-100 μs) are required to sufficiently reduce the statistical uncertainty. This may be further used for the determination of the relative, as well as absolute, configuration of chiral molecules.
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Affiliation(s)
- David Elsing
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Burkhard Luy
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131 Karlsruhe, Germany
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4
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Anklin C, Gil RR. Full configurational and conformational analysis of artemisinin by one-bond carbon-carbon residual dipolar couplings at natural abundance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:599-604. [PMID: 38558418 DOI: 10.1002/mrc.5443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Configurational and conformational analysis of the biologically relevant natural product artemisinin was conducted using carbon-carbon residual dipolar couplings (1DCC RDCs) at natural abundance. These RDCs were measured through the 2D-INADEQUATE NMR experiment using a sample aligned in a compressed poly (methyl methacrylate) (PMMA) gel swollen in CDCl3. Singular value decomposition (SVD) fitting analysis of all carbon-carbon bonds, 1DCC RDCs, in relation to the full configuration/conformational space (32 diastereoisomers) of artemisinin, unambiguously identified the correct configuration of artemisinin.
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Affiliation(s)
- Clemens Anklin
- Bruker BioSpin Corporation, Billerica, Massachusetts, USA
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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5
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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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6
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John M, Rüttger F. Multinuclear Residual Quadrupolar Couplings for Structure and Assignment. Chemphyschem 2024; 25:e202400068. [PMID: 38465709 DOI: 10.1002/cphc.202400068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 03/12/2024]
Abstract
Most stable isotopes have a nuclear spin >1/2, but the quadrupole interaction poses challenge on their detection by nuclear magnetic resonance (NMR). On the other hand, the quadrupole interaction is a rich source of structural information that may be exploited for solution NMR in the form of residual quadrupolar couplings (RQCs) of weakly oriented samples. While 2H RQCs are now well established for structure verification and enantiomeric discrimination of organic molecules, we will in this article highlight some recent work on RQCs of other nuclei (especially 7Li and 11B).
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Affiliation(s)
- Michael John
- Fakultät für Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077, Göttingen
| | - Franziska Rüttger
- Fakultät für Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, D-37077, Göttingen
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7
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Cantrelle FX, Boll E, Sinnaeve D. Making 1H- 1H Couplings More Accessible and Accurate with Selective 2DJ NMR Experiments Aided by 13C Satellites. Anal Chem 2024; 96:7056-7064. [PMID: 38666447 DOI: 10.1021/acs.analchem.4c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
1H-1H coupling constants are one of the primary sources of information for nuclear magnetic resonance (NMR) structural analysis. Several selective 2DJ experiments have been proposed that allow for their individual measurement at pure shift resolution. However, all of these experiments fail in the not uncommon case when coupled protons have very close chemical shifts. First, the coupling between protons with overlapping multiplets is inaccessible due to the inability of a frequency-selective pulse to invert just one of them. Second, the strong coupling condition affects the accuracy of coupling measurements involving third spins. These shortcomings impose a limit on the effectiveness of state-of-the-art experiments, such as G-SERF or PSYCHEDELIC. Here, we introduce two new and complementary selective 2DJ experiments that we coin SERFBIRD and SATASERF. These experiments overcome the aforementioned issues by utilizing the 13C satellite signals at natural isotope abundance, which resolves the chemical shift degeneracy. We demonstrate the utility of these experiments on the tetrasaccharide stachyose and the challenging case of norcamphor, for the latter achieving measurement of all JHH couplings, while only a few were accessible with PSYCHEDELIC. The new experiments are applicable to any organic compound and will prove valuable for configurational and conformational analyses.
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Affiliation(s)
- François-Xavier Cantrelle
- CNRS EMR 9002 ─ Integrative Structural Biology, F-59000 Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille UMR 1167 ─ RID-AGE ─ Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Emmanuelle Boll
- CNRS EMR 9002 ─ Integrative Structural Biology, F-59000 Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille UMR 1167 ─ RID-AGE ─ Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Davy Sinnaeve
- CNRS EMR 9002 ─ Integrative Structural Biology, F-59000 Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille UMR 1167 ─ RID-AGE ─ Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
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8
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Tichotová MC, Tučková L, Kocek H, Růžička A, Straka M, Procházková E. Exploring the impact of alignment media on RDC analysis of phosphorus-containing compounds: a molecular docking approach. Phys Chem Chem Phys 2024; 26:2016-2024. [PMID: 38126374 DOI: 10.1039/d3cp04099b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Residual dipolar couplings (RDCs) are employed in NMR analysis when conventional methods, such as J-couplings and nuclear Overhauser effects (NOEs) fail. Low-energy (optimized) conformers are often used as input structures in RDC analysis programs. However, these low-energy structures do not necessarily resemble conformations found in anisotropic environments due to interactions with the alignment medium, especially if the analyte molecules are flexible. Considering interactions with alignment media in RDC analysis, we developed and evaluated a molecular docking-based approach to generate more accurate conformer ensembles for compounds in the presence of the poly-γ-benzyl-L-glutamate alignment medium. We designed chiral phosphorus-containing compounds that enabled us to utilize 31P NMR parameters for the stereochemical analysis. Using P3D/PALES software to evaluate diastereomer discrimination, we found that our conformer ensembles outperform moderately the standard, low-energy conformers in RDC analysis. To further improve our results, we (i) averaged the experimental values of the molecular docking-based conformers by applying the Boltzmann distribution and (ii) optimized the structures through normal mode relaxation, thereby enhancing the Pearson correlation factor R and even diastereomer discrimination in some cases. Nevertheless, we presume that significant differences between J-couplings in isotropic and in anisotropic environments may preclude RDC measurements for flexible molecules. Therefore, generating conformer ensembles based on molecular docking enhances RDC analysis for mildly flexible systems while flexible molecules may require applying more advanced approaches, in particular approaches including dynamical effects.
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Affiliation(s)
- Markéta Christou Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Hugo Kocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice 532 10, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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9
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Li GW, Wang XJ, Shi SH, Liu LT, Li JQ, Sun H, Wu ZQ, Lei X. Polyarylisocyanides Derived from an Alkyne-Pd(II) Catalyst as Robust Alignment Media with Excellent Enantiodiscimination. Anal Chem 2023; 95:18850-18858. [PMID: 38091507 DOI: 10.1021/acs.analchem.3c04240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
The development of chiral alignment media for measuring anisotropic NMR parameters provides an opportunity to determine the absolute configuration of chiral molecules without the need for derivatization. However, chiral alignment media with a high and robust enantiodiscriminating property for a wide range of chiral molecules are still scarce. In this study, we synthesized cholesterol-end-functionalized helical polyisocyanides from a chiral monomer using a cholesterol-based alkyne-Pd(II) initiator. These stereoregular polyisocyanides form stable and weak anisotropic lyotropic liquid crystals (LLCs) in dichloromethane systems, exhibiting highly optical activities in both single left- and right-handed helices. The preparation process of the media was straightforward, and the aligning property of the LLCs could be controlled by adjusting the concentration and temperature. Using the chiral polyisocyanides, we extracted the residual dipolar coupling for an enantiomeric pair of isopinocampheol (IPC), as well as a number of pharmaceutical molecules, demonstrating excellent enantiodiscriminating properties for a broad range of chiral compounds.
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Affiliation(s)
- Gao-Wei Li
- College of Chemistry and Chemical Engineering, Henan Engineering Research Center for Green Synthesis of Pharmaceuticals, Shangqiu Normal University, Shangqiu 476000, China
| | - Xiao-Juan Wang
- College of Chemistry and Chemical Engineering, Henan Engineering Research Center for Green Synthesis of Pharmaceuticals, Shangqiu Normal University, Shangqiu 476000, China
| | - Shuai-Hua Shi
- College of Chemistry and Chemical Engineering, Henan Engineering Research Center for Green Synthesis of Pharmaceuticals, Shangqiu Normal University, Shangqiu 476000, China
| | - Lan-Tao Liu
- College of Chemistry and Chemical Engineering, Henan Engineering Research Center for Green Synthesis of Pharmaceuticals, Shangqiu Normal University, Shangqiu 476000, China
| | - Jia-Qian Li
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Han Sun
- Research Unit of Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
| | - Zong-Quan Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xinxiang Lei
- State Key Laboratory of Applied Organic Chemistry, Lanzhou Magnetic Resonance Center, College of Chemistry and Chemi-cal Engineering, Lanzhou University, Lanzhou 730000, China
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
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10
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Silva Elipe MV, Ndukwe IE, Navarro-Vázquez A. Anisotropic NMR data acquisition with a prototype 400 MHz cryogen-free NMR spectrometer. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:530-543. [PMID: 37530063 DOI: 10.1002/mrc.5380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
High-temperature superconducting (HTS) materials have recently been incorporated into the construction of HTS cryogen-free magnets for nuclear magnetic resonance (NMR) spectroscopy. These HTS NMR spectrometers do not require liquid cryogens, thereby providing significant cost savings and facilitating easy integration into chemistry laboratories. However, the optimal performance of these HTS magnets against standard cryogen NMR magnets must be evaluated, especially with demanding modern NMR applications such as NMR in anisotropic media. The stability of the HTS magnets over time and their performance with complex pulse sequence experiments are the main unknown factors of this new technology. In this study, we evaluate the utility of our prototype 400 MHz cryogen-free power-driven HTS NMR spectrometer, installed in the fumehood of a chemistry laboratory, for stereochemical analysis of three commercial natural products (artemisinin, artemether, and dihydroartemisinin) via measurement of anisotropic NMR data, in particular, residual dipolar couplings. The accuracy of measurement of the anisotropic NMR data with the HTS magnet spectrometer is evaluated through the CASE-3D fitting protocol, as implemented in the Mestrenova-StereoFitter software program.
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Affiliation(s)
| | | | - Armando Navarro-Vázquez
- Departmento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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11
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McCalpin SD, Fu R, Ravula T, Wu G, Ramamoorthy A. Magnetically aligned nanodiscs enable direct measurement of 17O residual quadrupolar coupling for small molecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107341. [PMID: 36473327 DOI: 10.1016/j.jmr.2022.107341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The use of 17O in NMR spectroscopy for structural studies has been limited due to its low natural abundance, low gyromagnetic ratio, and quadrupolar relaxation. Previous solution 17O work has primarily focused on studies of liquids where the 17O quadrupolar coupling is averaged to zero by isotropic molecular tumbling, and therefore has ignored the structural information contained in this parameter. Here, we use magnetically aligned polymer nanodiscs as an alignment medium to measure residual quadrupolar couplings (RQCs) for 17O-labelled benzoic acid in the aqueous phase. We show that increasing the magnetic field strength improves spectral sensitivity and resolution and that each satellite peak of the expected pentet pattern resolves clearly at 18.8 T. We observed no significant dependence of the RQC magnitudes on the magnetic field strength. However, changing the orientation of the alignment medium alters the RQC by a consistent factor, suggesting that 17O RQCs measured in this way can provide reliable orientational information for elucidations of molecular structures.
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Affiliation(s)
- Samuel D McCalpin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Thirupathi Ravula
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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12
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Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2 N-1 Diastereomers. JOURNAL OF NATURAL PRODUCTS 2022; 85:1837-1849. [PMID: 35820115 DOI: 10.1021/acs.jnatprod.2c00427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.
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Affiliation(s)
- Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar- und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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13
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Li XL, Ru T, Navarro-Vázquez A, Lindemann P, Nazaré M, Li XW, Guo YW, Sun H. Weizhouochrones: Gorgonian-Derived Symmetric Dimers and Their Structure Elucidation Using Anisotropic NMR Combined with DP4+ Probability and CASE-3D. JOURNAL OF NATURAL PRODUCTS 2022; 85:1730-1737. [PMID: 35792821 DOI: 10.1021/acs.jnatprod.2c00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Natural product dimers have intriguing structural features and often have remarkable pharmacological activities. We report here two uncommon marine gorgonian-derived symmetric dimers, weizhouochrones A (1) and B (2), with indenone-derived monomers, that were isolated from the coral Anthogorgia ochracea collected from the South China Sea. These dimers are difficult targets for structure elucidation that solely relies upon conventional NMR data such as NOEs and J-couplings. Here, to explore the application of emerging methods on the structure elucidation of challenging molecules, we explored a number of different anisotropic and computational NMR approaches. The measurements of anisotropic NMR parameters of weizhouochrone A, including residual dipolar couplings (RDCs) and residual chemical shift anisotropy (RCSA), allowed us to successfully determine the planar structure and its relative configuration. This result was corroborated by a computational NMR analysis based on DP4+ probability and computer-assisted 3D structure elucidation (CASE-3D).
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Affiliation(s)
- Xiao-Lu Li
- Group of Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Tong Ru
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Peter Lindemann
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Marc Nazaré
- Group of Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | - Xu-Wen Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Han Sun
- Institute of Chemistry, Technical University of Berlin, Berlin 10623, Germany
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14
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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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15
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Schirra DS, Götz P, Lehmann M, Thiele CM. Atropisomerism in a polyglutamate-based thermoresponsive alignment medium. Chem Commun (Camb) 2022; 58:7511-7514. [PMID: 35708488 DOI: 10.1039/d2cc01982e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure elucidation via residual dipolar couplings (RDCs) relies on alignment media. We report on lyotropic liquid crystals (LLCs) of poly-γ-p-biphenyl(2'-methoxy-2-methyl)methyl-L-glutamate (PBPM3LG). Temperature dependent atropisomerism within the biphenyl group enables the acquisition of multiple RDC-datasets within one sample.
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Affiliation(s)
- Dominic S Schirra
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Research and Laboratory Center M3, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Philipp Götz
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Research and Laboratory Center M3, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Matthias Lehmann
- Institute for Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Research and Laboratory Center M3, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
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16
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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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17
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Schirra DS, Jeziorowski S, Lehmann M, Thiele CM. Thermoreversible Gelation of Homopolyglutamates PBPMLG, PBPELG, and PBPHLG: Another Step toward de Novo RDC-Based Structure Elucidation. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dominic S. Schirra
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Sharon Jeziorowski
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Matthias Lehmann
- Institute for Organic Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
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18
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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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19
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Berdagué P, Gouilleux B, Noll M, Immel S, Reggelin M, Lesot P. Study and quantification of enantiodiscrimination power of four polymeric chiral LLCs using NAD 2D-NMR. Phys Chem Chem Phys 2022; 24:7338-7348. [DOI: 10.1039/d1cp04915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identifying and understanding the role of key molecular factors involved in the orientation/discrimination phenomena of analytes in polymer-based chiral liquid crystals (CLCs) are essential tasks for optimizing computational predictions (molecular...
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20
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Immel S, Köck M, Reggelin M. NMR-Based Configurational Assignments of Natural Products: Gibbs Sampling and Bayesian Inference Using Floating Chirality Distance Geometry Calculations. Mar Drugs 2021; 20:14. [PMID: 35049868 PMCID: PMC8781118 DOI: 10.3390/md20010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
Floating chirality restrained distance geometry (fc-rDG) calculations are used to directly evolve structures from NMR data such as NOE-derived intramolecular distances or anisotropic residual dipolar couplings (RDCs). In contrast to evaluating pre-calculated structures against NMR restraints, multiple configurations (diastereomers) and conformations are generated automatically within the experimental limits. In this report, we show that the "unphysical" rDG pseudo energies defined from NMR violations bear statistical significance, which allows assigning probabilities to configurational assignments made that are fully compatible with the method of Bayesian inference. These "diastereomeric differentiabilities" then even become almost independent of the actual values of the force constants used to model the restraints originating from NOE or RDC data.
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Affiliation(s)
- Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut für Polar-und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany;
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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21
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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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22
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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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23
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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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24
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Recchia MJJ, Cohen RD, Liu Y, Sherer EC, Harper JK, Martin GE, Williamson RT. "One-Shot" Measurement of Residual Chemical Shift Anisotropy Using Poly-γ-benzyl-l-glutamate as an Alignment Medium. Org Lett 2020; 22:8850-8854. [PMID: 33140974 DOI: 10.1021/acs.orglett.0c03225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A method for the measurement of residual chemical shift anisotropy in one experiment using a biphasic isotropic/anisotropic lyotropic liquid crystalline medium based on poly-γ-benzyl-l-glutamate as the alignment medium is presented. This approach is demonstrated on the model compound strychnine and neotricone, a depsidone natural product with a questionable structural assignment based on comparison with the closely related excelsione and in-depth density functional theory calculations.
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Affiliation(s)
- Michael J J Recchia
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Ryan D Cohen
- Analytical Research & Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - Yizhou Liu
- Analytical Research & Development, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Edward C Sherer
- Analytical Research & Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Gary E Martin
- Department of Chemistry, Seton Hall University, South Orange, New Jersey 07079, United States
| | - R Thomas Williamson
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
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25
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Sager E, Tzvetkova P, Gossert AD, Piechon P, Luy B. Determination of Configuration and Conformation of a Reserpine Derivative with Seven Stereogenic Centers Using Molecular Dynamics with RDC-Derived Tensorial Constraints*. Chemistry 2020; 26:14435-14444. [PMID: 32744785 PMCID: PMC7702126 DOI: 10.1002/chem.202002642] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/22/2020] [Indexed: 11/11/2022]
Abstract
NMR-based determination of the configuration of complex molecules containing many stereocenters is often not possible using traditional NOE data and coupling patterns. Making use of residual dipolar couplings (RDCs), we were able to determine the relative configuration of a natural product containing seven stereocenters, including a chiral amine lacking direct RDC data. To identify the correct relative configuration out of 32 possible ones, experimental RDCs were used in three different approaches for data interpretation: by fitting experimental data based singular value decomposition (SVD) using a single alignment tensor and either (i) a single conformer or (ii) multiple conformers, or alternatively (iii) using molecular dynamics simulations with tensorial orientational constraints (MDOC). Even though in all three approaches one and the same configuration could be selected and clear discrimination between possible configurations was achieved, the experimental data was not fully satisfied by the methods based on single tensor approaches. While these two approaches are faster, only MDOC is able to fully reproduce experimental results, as the obtained conformational ensemble adequately covers the conformational space necessary to describe the molecule with inherent flexibility.
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Affiliation(s)
- Emine Sager
- Institut für Organische ChemieKarlsruher Institut für Technologie (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
| | - Pavleta Tzvetkova
- Institut für Biologische Grenzflächen 4—Magnetische ResonanzKarlsruher Institut für Technologie (KIT)Postfach 364076021KarlsruheGermany
| | - Alvar D. Gossert
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
- Institut für Molekularbiologie und BiophysikETH Zürich8093ZürichSwitzerland
| | - Philippe Piechon
- Novartis Pharma AGNovartis Institutes for Biomedical Research4002BaselSwitzerland
| | - Burkhard Luy
- Institut für Organische ChemieKarlsruher Institut für Technologie (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institut für Biologische Grenzflächen 4—Magnetische ResonanzKarlsruher Institut für Technologie (KIT)Postfach 364076021KarlsruheGermany
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26
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Qin S, Jiang Y, Sun H, Liu H, Zhang A, Lei X. Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid‐Crystalline‐Based Medium. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Si‐Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Yan Jiang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Han Sun
- Section of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) 13125 Berlin Germany
| | - Han Liu
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ai‐Qing Zhang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Xinxiang Lei
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
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27
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Qin S, Jiang Y, Sun H, Liu H, Zhang A, Lei X. Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid‐Crystalline‐Based Medium. Angew Chem Int Ed Engl 2020; 59:17097-17103. [DOI: 10.1002/anie.202007243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Si‐Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Yan Jiang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Han Sun
- Section of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) 13125 Berlin Germany
| | - Han Liu
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ai‐Qing Zhang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Xinxiang Lei
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
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28
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Köck M, Reggelin M, Immel S. The Advanced Floating Chirality Distance Geometry Approach-How Anisotropic NMR Parameters Can Support the Determination of the Relative Configuration of Natural Products. Mar Drugs 2020; 18:md18060330. [PMID: 32599876 PMCID: PMC7344786 DOI: 10.3390/md18060330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 11/16/2022] Open
Abstract
The configurational analysis of complex natural products by NMR spectroscopy is still a challenging task. The assignment of the relative configuration is usually carried out by analysis of interproton distances from NOESY or ROESY spectra (qualitative or quantitative) and scalar (J) couplings. About 15 years ago, residual dipolar couplings (RDCs) were introduced as a tool for the configurational determination of small organic molecules. In contrast to NOEs/ROEs which are local parameters (distances up to 400 pm can be detected for small organic molecules), RDCs are global parameters which allow to obtain structural information also from long-range relationships. RDCs have the disadvantage that the sample needs a setup in an alignment medium in order to obtain the required anisotropic environment. Here, we will discuss the configurational analysis of five complex natural products: axinellamine A (1), tetrabromostyloguanidine (2), 3,7-epi-massadine chloride (3), tubocurarine (4), and vincristine (5). Compounds 1-3 are marine natural products whereas 4 and 5 are from terrestrial sources. The chosen examples will carefully work out the limitations of NOEs/ROEs in the configurational analysis of natural products and will also provide an outlook on the information obtained from RDCs.
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Affiliation(s)
- Matthias Köck
- Alfred-Wegener-Institut für Polar-und Meeresforschung in der Helmholtz-Gemeinschaft, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Michael Reggelin
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Stefan Immel
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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29
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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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30
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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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31
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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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32
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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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33
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Tzvetkova P, Sternberg U, Gloge T, Navarro-Vázquez A, Luy B. Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints. Chem Sci 2019; 10:8774-8791. [PMID: 31803450 PMCID: PMC6849632 DOI: 10.1039/c9sc01084j] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/19/2019] [Indexed: 12/27/2022] Open
Abstract
Residual dipolar couplings (RDCs) and other residual anisotropic NMR parameters provide valuable structural information of high quality and quantity, bringing detailed structural models of flexible molecules in solution in reach. The corresponding data interpretation so far is directly or indirectly based on the concept of a molecular alignment tensor, which, however, is ill-defined for flexible molecules. The concept is typically applied to a single or a small set of lowest energy structures, ignoring the effect of vibrational averaging. Here, we introduce an entirely different approach based on time averaged molecular dynamics with dipolar couplings as tensorial orientational restraints that can be used to solve structural problems in molecules of any size without the need of introducing an explicit molecular alignment tensor into the computation. RDC restraints are represented by their full 3D interaction tensor in the laboratory frame, for which pseudo forces are calculated using a secular dipolar Hamiltonian as the target. The resulting rotational averaging of each individual tensorial restraint leads to structural ensembles that best fulfil the experimental data. Using one-bond RDCs, the approach has been implemented in the force field procedures of the program COSMOS and extensively tested. A concise theoretical introduction, including the special treatment of force fields for stable and fast MD simulations, as well as applications regarding configurational analyses of small to medium-sized organic molecules with different degrees of flexibility, is given. The observed results are discussed in detail.
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Affiliation(s)
- Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Ulrich Sternberg
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Thomas Gloge
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Armando Navarro-Vázquez
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany . ;
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34
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Di Pietro ME, Sternberg U, Luy B. Molecular Dynamics with Orientational Tensorial Constraints: A New Approach to Probe the Torsional Angle Distributions of Small Rotationally Flexible Molecules. J Phys Chem B 2019; 123:8480-8491. [PMID: 31502838 DOI: 10.1021/acs.jpcb.9b07008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The potential of residual dipolar couplings (RDCs) in conformational studies of small molecules is now widely recognized, but current theoretical approaches for their interpretation have several limitations and there is still the need for a general method to probe the torsional angle distributions applicable to any rotationally flexible molecule. Molecular dynamics simulations with RDC-based orientational tensorial constraints (MDOC), implemented in the software COSMOS, are presented here as a conceptually new strategy. For the cases of the fluorinated anti-inflammatory drug diflunisal and the disaccharide cellobiose, we demonstrate that MDOC simulations with one-bond RDCs as tensorial constraints unveil torsion distributions and allow the determination of relative configuration in the presence of rotational flexibility. The independence of the initial structure or any a priori assumption as well as the possibility to combine different experimental constraints represent features, which make the COSMOS software a promising tool for the investigation of torsional angle distributions of flexible molecules, regardless of their size and degree of freedom.
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Affiliation(s)
- Maria E Di Pietro
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Ulrich Sternberg
- COSMOS GbR , Jena 07743 , Germany.,Research Partner , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany
| | - Burkhard Luy
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Karlsruhe 76131 , Germany.,Institute for Biological Interfaces 4-Magnetic Resonance , Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen 76021 , Germany
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35
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Hirschmann M, Schwab M, Thiele CM. Molecular Weights: The Key for Lyotropic Liquid Crystalline Phases of Poly-β-benzyl-l-aspartate. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Max Hirschmann
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Mira Schwab
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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36
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Meier MAR, Barner-Kowollik C. A New Class of Materials: Sequence-Defined Macromolecules and Their Emerging Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806027. [PMID: 30600565 DOI: 10.1002/adma.201806027] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/17/2018] [Indexed: 06/09/2023]
Abstract
Emerging applications of a new class of materials, sequence-defined macromolecules, are explored. Such molecularly highly defined macromolecules require stringent synthesis and purification procedures, yet offer unprecedented application possibilities. The first examples of molecular data storage and related technologies are already starting to emerge today. From a more fundamental point of view, such macromolecules offer a unique opportunity to determine quantitative structure-property relationships (QSPR), which critically aids in designing materials with applications ranging from catalysis to artificial enzymes.
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Affiliation(s)
- Michael A R Meier
- Institute of Organic Chemistry (IOC), Materialwissenschaftliches Zentrum (MZE), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, 76131, Karlsruhe, Germany
| | - Christopher Barner-Kowollik
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD, 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131, Karlsruhe, Germany
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37
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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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38
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Immel S, Köck M, Reggelin M. Configurational analysis by residual dipolar couplings: A critical assessment of diastereomeric differentiabilities. Chirality 2019; 31:384-400. [PMID: 30916829 DOI: 10.1002/chir.23065] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 11/06/2022]
Abstract
Two independent statistical models for evaluating the certainties of configurational assignments of compounds based on nuclear magnetic resonance (NMR) data are evaluated and compared. Both methods yield weights or probabilities with which two or more structure models (constitutional or configurational isomers or even conformers) could be differentiated based on experimental parameters. Although this paper focusses on the use of residual dipolar couplings (RDCs) for the differentiation of diastereomers, the concept can be expanded to any set of experimental NMR-derived parameters. It is demonstrated that highly reliable configurational assignments crucially must depend on thorough statistical analysis, which is frequently neglected in the literature.
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Affiliation(s)
- Stefan Immel
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut (AWI), Helmholtz-Zentrum für Polar- und Meeresforschung, Sektion Ökologische Chemie, Bremerhaven, Germany.,Helmholtz-Zentrum für Infektionsforschung (HZI), Abteilung Chemische Biologie, Braunschweig, Germany
| | - Michael Reggelin
- Clemens Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
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39
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Knoll K, Leyendecker M, Thiele CM. l
‐Valine Derivatised 1,3,5‐Benzene‐Tricarboxamides as Building Blocks for a New Supramolecular Organogel‐Like Alignment Medium. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kevin Knoll
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
| | - Martin Leyendecker
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Technische Universität Darmstadt Clemens‐Schöpf Institut für Organische Chemie und Biochemie Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
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40
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Menna M, Imperatore C, Mangoni A, Della Sala G, Taglialatela-Scafati O. Challenges in the configuration assignment of natural products. A case-selective perspective. Nat Prod Rep 2019; 36:476-489. [DOI: 10.1039/c8np00053k] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An overview by a case study approach on the currently available methods for the configurational analysis of natural products.
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Affiliation(s)
- Marialuisa Menna
- Department of Pharmacy
- University of Naples Federico II
- 80131 Napoli
- Italy
| | | | - Alfonso Mangoni
- Department of Pharmacy
- University of Naples Federico II
- 80131 Napoli
- Italy
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41
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Application of anisotropic NMR parameters to the confirmation of molecular structure. Nat Protoc 2018; 14:217-247. [DOI: 10.1038/s41596-018-0091-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Görling B, Bermel W, Bräse S, Luy B. Homonuclear decoupling by projection reconstruction. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:1006-1020. [PMID: 30058249 DOI: 10.1002/mrc.4784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/16/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Similar to J-resolved spectroscopy, also, heteronuclear multiple bond correlation (HMBC), heteronuclear single bond correlation (HSBC), and heteronuclear multiple quantum coherence (HMQC) types of correlation experiments result in homonuclear tilted multiplet patterns. On the example of the high-resolution heteronuclear single bond correlation (HR-HSBC) pulse sequence, it is shown how the tilt angle can be varied within a wide range of positive and negative values. Projection along the tilt angles in all cases results in homonuclear decoupling. Using well-known projection reconstruction techniques, the different tilt angles can be used to reconstruct a homonuclear decoupled two-dimensional correlation spectrum. The concept is proven and further refined by segmental projection reconstruction and the use of a clean in-phase heteronuclear single quantum correlation (CLIP-HSQC) spectrum with an effective zero tilt angle for further filtering. The proof of principle, its application to one-bond coupling measurement, as well as a basic HMBC, and a detailed discussion with comparison to other homodecoupling techniques are given.
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Affiliation(s)
- Benjamin Görling
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Bruker Biospin GmbH, Rheinstetten, Germany
| | | | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Burkhard Luy
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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43
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Schwab M, Schmidts V, Thiele CM. Thermoresponsive Alignment Media in NMR Spectroscopy: Helix Reversal of a Copolyaspartate at Ambient Temperatures. Chemistry 2018; 24:14373-14377. [PMID: 29999196 DOI: 10.1002/chem.201803540] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 11/07/2022]
Abstract
Poly(aspartic acid esters) are known to form either right-or left-handed α-helices depending on the ester group in the side chain, on solvent and/or on temperature. Polyphenethyl-l-aspartates (PPLA) exhibit a helix reversal from the right- to the left-handed form with increasing temperature. We have recently reported the application of polyphenethylaspartates as helically chiral alignment media. The thermoresponsivity observed for these polymers offers the possibility to measure different orientations of analytes before and after helix reversal of the alignment medium at 373 K. Herein we present a synthesized copolymer of phenethyl- and benzylaspartate as a new alignment medium undergoing this helix reversal at 303-313 K. Thus, the measurement of residual dipolar couplings (RDC) before and after the helix reversal is allowed for at ambient temperatures. A complete sign change of all 1 H-13 C RDCs was observed, which is close to the highest possible difference in NMR spectra.
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Affiliation(s)
- Mira Schwab
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
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Immel S, Köck M, Reggelin M. Configurational Analysis by Residual Dipolar Coupling Driven Floating Chirality Distance Geometry Calculations. Chemistry 2018; 24:13918-13930. [PMID: 29999551 DOI: 10.1002/chem.201802800] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Indexed: 11/06/2022]
Abstract
A new method implemented into a computer program (ConArch+ ) has been developed and applied to demonstrate the successful implementation of residual dipolar couplings (RDCs) in distance geometry (DG) calculations for the configurational assignment of chiral compounds. Unlike established protocols, the new approach combines floating chirality (fc) in 4D- and 3D-distance bounds driven dynamics (DDD) calculations with structural information from RDCs. Thus, relative configurations of chiral compounds were generated only by observables (e.g., NOEs, RDCs) rendering tedious evaluations of calculated structures against RDCs obsolete. We demonstrate the potential of this novel procedure by the simultaneous determination of the configuration and the conformation of three natural products, (-)-isopinocampheol (1), tubocurarine (2), and vincristine (3), as well as for diisopropylidene-β-d-fructopyranose (4).
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Affiliation(s)
- Stefan Immel
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
| | - Matthias Köck
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany.,Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Abteilung Mikrobielle Naturstoffe, Universität des Saarlandes, Universitätscampus E8.1, 66123, Saarbrücken, Germany
| | - Michael Reggelin
- Technische Universität Darmstadt, Clemens Schöpf Institut für Organische Chemie und Biochemie, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany
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Rigling C, Kisunzu JK, Duschmalé J, Häussinger D, Wiesner M, Ebert MO, Wennemers H. Conformational Properties of a Peptidic Catalyst: Insights from NMR Spectroscopic Studies. J Am Chem Soc 2018; 140:10829-10838. [PMID: 30106584 DOI: 10.1021/jacs.8b05459] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptides have become valuable as catalysts for a variety of different reactions, but little is known about the conformational properties of peptidic catalysts. We investigated the conformation of the peptide H-dPro-Pro-Glu-NH2, a highly reactive and stereoselective catalyst for conjugate addition reactions, and the corresponding enamine intermediate in solution by NMR spectroscopy and computational methods. The combination of nuclear Overhauser effects (NOEs), residual dipolar couplings (RDCs), J-couplings, and temperature coefficients revealed that the tripeptide adopts a single predominant conformation in its ground state. The structure is a type I β-turn, which gains stabilization from three hydrogen bonds that are cooperatively formed between all functional groups (secondary amine, carboxylic acid, amides) within the tripeptide. In contrast, the conformation of the enamine intermediate is significantly more flexible. The conformational ensemble of the enamine is still dominated by the β-turn, but the backbone and the side chain of the glutamic acid residue are more dynamic. The key to the switch between rigidity and flexibility of the peptidic catalyst is the CO2H group in the side chain of the glutamic acid residue, which acts as a lid that can open and close. As a result, the peptidic catalyst is able to adapt to the structural requirements of the intermediates and transition states of the catalytic cycle. These insights might explain the robustness and high reactivity of the peptidic catalyst, which exceeds that of other secondary amine-based organocatalysts. The data suggest that a balance between rigidity and flexibility, which is reminiscent of the dynamic nature of enzymes, is beneficial for peptidic catalysts and other synthetic catalysts.
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Affiliation(s)
- Carla Rigling
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jessica K Kisunzu
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jörg Duschmalé
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland.,Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Markus Wiesner
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Helma Wennemers
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
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46
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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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Lakshmi JK, Pattnaik B, Kavitha R, Mallavadhani UV, Jagadeesh B. Conformation of flexibly linked triterpene dimers by using RDC-enhanced NMR spectroscopy. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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48
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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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49
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Niklas T, Steinmetzger C, Rüttger F, Stalke D, John M. Distinct alignment of benzene derivatives in stretched polystyrene and polybutylacrylate gels: Specific polymer-solute interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:1084-1090. [PMID: 28736823 DOI: 10.1002/mrc.4633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 06/07/2023]
Abstract
We have measured the alignment of a range of benzene derivatives in cross-linked polystyrene and poly(butyl acrylate) using a small number of residual dipolar couplings and simple geometric considerations. For apolar solutes in polystyrene and protic solutes in poly(butyl acrylate), the preferred molecular orientation does not coincide with the longest molecular axis (steric aligment). This behavior may be explained by specific π-π and hydrogen bonding interactions between solute and polymer, respectively, the latter being confirmed by molecular dynamics simulations.
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Affiliation(s)
- T Niklas
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - C Steinmetzger
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - F Rüttger
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - D Stalke
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - M John
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
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50
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Schwab M, Herold D, Thiele CM. Polyaspartates as Thermoresponsive Enantiodifferentiating Helically Chiral Alignment Media for Anisotropic NMR Spectroscopy. Chemistry 2017; 23:14576-14584. [DOI: 10.1002/chem.201702884] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Mira Schwab
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Dominik Herold
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
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