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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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2
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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. [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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3
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Gouilleux B, Moussallieh FM, Lesot P. Anisotropic 1 H STD-NMR Spectroscopy: Exploration of Enantiomer-Polypeptide Interactions in Chiral Oriented Environments. Chemphyschem 2023; 24:e202200508. [PMID: 36196851 DOI: 10.1002/cphc.202200508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/01/2022] [Indexed: 11/07/2022]
Abstract
We explore and report for the first time the use of 1 H saturation transfer difference NMR experiments (STD-NMR) in weakly aligning chiral anisotropic media to identify the hydrogen sites of enantiomers of small chiral molecules interacting with the side-chain of poly-γ-benzyl-l-glutamate (PBLG), a helically chiral polypeptide polymer. The first experimental results obtained on three model mono-stereogenic compounds outcomes are highly promising and demonstrate the possibility to track down possible differences of spatial position of enantiomers at the vicinity of the polymer side-chain. Anisotropic STD experiments appear to be well suited for rapid screening of chiral analytes that bind favorably to orienting polymeric systems, while providing new insights into the mechanism of enantio-discrimination without resorting to the time-consuming determination of molecular order parameters.
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Affiliation(s)
- Boris Gouilleux
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Francois-Marie Moussallieh
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15, rue du Doyen Georges Poitou, 91405, Orsay cedex, France
| | - Philippe Lesot
- Université Paris-Saclay, UFR d'Orsay, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Bât. 410, 15, rue du Doyen Georges Poitou, 91405, Orsay cedex, France.,Centre National de la Recherche Scientifique (CNRS), 3, rue Michel Ange, 75016, Paris, France
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4
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Liu Y, Ndukwe IE, Reibarkh M, Martin GE, Williamson RT. Prediction of anisotropic NMR data without knowledge of alignment medium structure by surface decomposition. Phys Chem Chem Phys 2022; 24:20164-20182. [PMID: 35996986 DOI: 10.1039/d2cp02621j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prediction of anisotropic NMR data directly from solute-medium interaction is of significant theoretical and practical interest, particularly for structure elucidation, configurational analysis and conformational studies of complex organic molecules and natural products. Current prediction methods require an explicit structural model of the alignment medium: a requirement either impossible or impractical on a scale necessary for small organic molecules. Here we formulate a comprehensive mathematical framework for a parametrization protocol that deconvolutes an arbitrary surface of the medium into several simple local landscapes that are distributed over the medium's surface by specific orientational order parameters. The shapes and order parameters of these local landscapes are determined via fitting that maximizes the congruence between experimentally determined anisotropic NMR measurables and their predicted counterparts, thus avoiding the need for an a priori knowledge of the global medium morphology. This method achieves substantial improvements in the accuracy of predicted anisotropic NMR values compared to current methods, as demonstrated herein with sixteen natural products. Furthermore, because this formalism extracts structural commonalities of the medium by combining anisotropic NMR data from different compounds, its robustness and accuracy are expected to improve as more experimental data become available for further re-optimization of fitting parameters.
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Affiliation(s)
- Yizhou Liu
- Analytical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, CT, 06340, USA.
| | - Ikenna E Ndukwe
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Gary E Martin
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - R Thomas Williamson
- Analytical Research and Development, Merck & Co. Inc., 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
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5
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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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Aroulanda C, Lesot P. Molecular enantiodiscrimination by NMR spectroscopy in chiral oriented systems: Concept, tools, and applications. Chirality 2021; 34:182-244. [PMID: 34936130 DOI: 10.1002/chir.23386] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
The study of enantiodiscriminations in relation to various facets of enantiomorphism (chirality/prochirality) and/or molecular symmetry is an exciting area of modern organic chemistry and an ongoing challenge for nuclear magnetic resonance (NMR) spectroscopists who have developed many useful analytical approaches to solve stereochemical problems. Among them, the anisotropic NMR using chiral aligning solvents has provided a set of new and original tools by making accessible all intramolecular, order-dependent NMR interactions (anisotropic interactions), such as residual chemical shift anisotropy (RCSA), residual dipolar coupling (RDC), and residual quadrupolar coupling (RQC) for spin I > 1/2, while preserving high spectral resolution. The force of NMR in enantiopure, oriented solvents lies on its ability to orient differently in average on the NMR timescale enantiomers of chiral molecules and enantiotopic elements of prochiral ones, leading distinct NMR spectra or signals to be detected. In this compendium mainly written for all chemists playing with (pro)chirality, we overview various key aspects of NMR in weakly aligning chiral solvents as the lyotropic liquid crystals (LLCs), in particular those developed in France to study (pro)chiral compounds in relation with chemists needs: study of enantiopurity of mixture, stereochemistry, natural isotopic fractionation, as well as molecular conformation and configuration. Key representative examples covering the diversity of enantiomorphism concept, and the main and most recent applications illustrating the analytical potential of this NMR in polypeptide-based chiral liquid crystals (CLCs) are examined. The latest analytical strategy developed to determine in-solution conformational distribution of flexibles solutes using NMR in polypeptide-based aligned solvents is also proposed.
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Affiliation(s)
- Christie Aroulanda
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
| | - Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris-Saclay, Orsay cedex, France
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7
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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: 7] [Impact Index Per Article: 1.8] [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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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Determination of Complex Small-Molecule Structures Using Molecular Alignment Simulation. Angew Chem Int Ed Engl 2020; 59:6172-6176. [PMID: 31971323 PMCID: PMC7187346 DOI: 10.1002/anie.202000311] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/23/2020] [Indexed: 11/12/2022]
Abstract
Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy-based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule-specific anisotropic NMR parameters. The quantitative correlation uses an accurate three-dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ-benzyl-l-glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.
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Affiliation(s)
- Alain Ibáñez de Opakua
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
| | - Frederik Klama
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Complex Carbohydrate Research CenterUniversity of GeorgiaAthensGA30602USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry and BiochemistrySeton Hall UniversitySouth OrangeNJ07079USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway)Merck & Co. Inc.KenilworthNJUSA
- Department of Chemistry & BiochemistryUniversity of North Carolina WilmingtonWilmingtonNC28409USA
| | - Markus Zweckstetter
- Structural Biology in DementiaGerman Center for Neurodegenerative Diseases (DZNE)Von-Siebold-Strasse 3a37075GöttingenGermany
- Department for NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
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9
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Ibáñez de Opakua A, Klama F, Ndukwe IE, Martin GE, Williamson RT, Zweckstetter M. Bestimmung komplexer kleiner Molekülstrukturen mittels molekularer Ausrichtungssimulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alain Ibáñez de Opakua
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
| | - Frederik Klama
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
| | - Ikenna E. Ndukwe
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Complex Carbohydrate Research CenterUniversity of Georgia Athens GA 30602 USA
| | - Gary E. Martin
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry and BiochemistrySeton Hall University South Orange NJ 07079 USA
| | - R. Thomas Williamson
- Analytical Research & Development (Rahway), Merck & Co. Inc. Kenilworth NJ USA
- Department of Chemistry & BiochemistryUniversity of North Carolina Wilmington Wilmington NC 28409 USA
| | - Markus Zweckstetter
- Translationale Strukturelle Biologie der DemenzDeutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Von-Siebold-Str. 3a 37075 Göttingen Deutschland
- Abteilung für NMR-basierte StrukturbiologieMax-Planck-Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Deutschland
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Lesot P, Aroulanda C, Berdagué P, Meddour A, Merlet D, Farjon J, Giraud N, Lafon O. Multinuclear NMR in polypeptide liquid crystals: Three fertile decades of methodological developments and analytical challenges. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 116:85-154. [PMID: 32130960 DOI: 10.1016/j.pnmrs.2019.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy of oriented samples makes accessible residual anisotropic intramolecular NMR interactions, such as chemical shift anisotropy (RCSA), dipolar coupling (RDC), and quadrupolar coupling (RQC), while preserving high spectral resolution. In addition, in a chiral aligned environment, enantiomers of chiral molecules or enantiopic elements of prochiral compounds adopt different average orientations on the NMR timescale, and hence produce distinct NMR spectra or signals. NMR spectroscopy in chiral aligned media is a powerful analytical tool, and notably provides unique information on (pro)chirality analysis, natural isotopic fractionation, stereochemistry, as well as molecular conformation and configuration. Significant progress has been made in this area over the three last decades, particularly using polypeptide-based chiral liquid crystals (CLCs) made of organic solutions of helically chiral polymers (as PBLG) in organic solvents. This review presents an overview of NMR in polymeric LCs. In particular, we describe the theoretical tools and the major NMR methods that have been developed and applied to study (pro)chiral molecules dissolved in such oriented solvents. We also discuss the representative applications illustrating the analytical potential of this original NMR tool. This overview article is dedicated to thirty years of original contributions to the development of NMR spectroscopy in polypeptide-based chiral liquid crystals.
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Affiliation(s)
- Philippe Lesot
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France; Centre National de la Recherche Scientifique (CNRS), France.
| | - Christie Aroulanda
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Philippe Berdagué
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Abdelkrim Meddour
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Denis Merlet
- Université Paris Sud/Université Paris-Saclay, UMR CNRS 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, ICMMO, Equipe RMN en Milieu Orienté, Bât. 410, 15 rue du Doyen Georges Poitou, F-91405 Orsay cedex, France
| | - Jonathan Farjon
- Centre National de la Recherche Scientifique (CNRS), France; Faculté des Sciences et Techniques de Nantes, UMR CNRS 6230, Chimie et Interdisciplinarité, Synthèse, Analyse, Modélisation, CEISAM, Equipe EBSI, BP 92208, 2 rue de la Houssinière, F-44322 Nantes cedex 3, France
| | - Nicolas Giraud
- Université Paris Descartes, Sorbonne Paris Cité, UMR CNRS 8601, Laboratory of Pharmacological and Toxicological Chemistry and Biochemistry, LPTCB, 45 rue des Saints Pères, F-75006 Paris, France
| | - Olivier Lafon
- Universite de Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR CNRS 8181, Unité de Catalyse et Chimie du Solide, UCCS, F-59000 Lille, France; Institut Universitaire de France (IUF), France
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11
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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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12
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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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13
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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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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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15
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Hansmann S, Schmidts V, Thiele CM. Synthesis of Poly-γ-S-2-methylbutyl-l-glutamate and Poly-γ-S-2-methylbutyl-d-glutamate and Their Use as Enantiodiscriminating Alignment Media in NMR Spectroscopy. Chemistry 2017; 23:9114-9121. [DOI: 10.1002/chem.201700699] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Stefanie Hansmann
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
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16
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Navarro-Vázquez A, Berdagué P, Lesot P. Integrated Computational Protocol for the Analysis of Quadrupolar Splittings from Natural-Abundance Deuterium NMR Spectra in (Chiral) Oriented Media. Chemphyschem 2017; 18:1252-1266. [DOI: 10.1002/cphc.201601423] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental; Universidade Federal de Pernambuco Cidade Universitária; CEP: 50 740-540 Recife PE Brazil
- Institute of Organic Chemistry and Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe German
| | - Philippe Berdagué
- RMN en Milieu Orienté; ICMMO; UMR CNRS 8182; Université Paris-Sud/Université Paris-Saclay; Bât. 410 91405 Orsay cedex France
| | - Philippe Lesot
- RMN en Milieu Orienté; ICMMO; UMR CNRS 8182; Université Paris-Sud/Université Paris-Saclay; Bât. 410 91405 Orsay cedex France
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17
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Schmidts V. Perspectives in the application of residual dipolar couplings in the structure elucidation of weakly aligned small molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:54-60. [PMID: 27743456 DOI: 10.1002/mrc.4543] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 05/28/2023]
Abstract
This perspective article aims to review the general methodology in the application of residual dipolar couplings (RDCs) in the structure elucidation of small molecules and give the author's view on challenges for future applications. Recent improvements in the availability of alignment media, new pulse sequences for the measurement of couplings and improvements in the analysis software have garnered widespread interest in the technique. However, further generalization is needed in order to make RDC analysis into a truly "routine" method. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
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18
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Al‐Massaedh “AA, Schmidt M, Pyell U, Reinscheid UM. Elucidation of the Enantiodiscrimination Properties of a Nonracemic Chiral Alignment Medium through Gel-based Capillary Electrochromatography: Separation of the Mefloquine Stereoisomers. ChemistryOpen 2016; 5:455-459. [PMID: 27777838 PMCID: PMC5062011 DOI: 10.1002/open.201600085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 11/07/2022] Open
Abstract
Enantiodiscrimination and enantioseparation are two highly important processes in chemistry, often performed by using NMR spectroscopy and chromatography. For a better understanding of the mechanistic details, the same system should be studied by both methods. In addition, isotropic and anisotropic NMR parameters should be obtained, the latter using alignment media so that residual dipolar couplings and chemical-shift anisotropies can be measured. Consequently, a chiral alignment medium was used for the first time in chiral gel-based capillary electrochromatography with the four stereoisomers of the antimalaria drug mefloquine as test compounds. Chromatographic data verify that enantiodiscrimination obtained with this alignment gel is caused by differences in the equilibrium constants related to associate formation. Hence, the chromatographic separation provides physicochemical data that form a basis for the understanding and optimization of alignment processes, and vice versa.
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Affiliation(s)
- “Ayat Allah” Al‐Massaedh
- Department of ChemistryUniversity of MarburgHans-Meerwein-Straße35032MarburgGermany
- Department of ChemistryFaculty of ScienceAl al-Bayt University25113MafraqJordan
| | - Manuel Schmidt
- Department of NMR-based Structural BiologyMax-Planck-Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Ute Pyell
- Department of ChemistryUniversity of MarburgHans-Meerwein-Straße35032MarburgGermany
| | - Uwe M. Reinscheid
- Department of NMR-based Structural BiologyMax-Planck-Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
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19
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Serhan Z, Aroulanda C, Lesot P. Investigation of Solute-Fiber Affinity and Orientational Ordering of Norbornadiene Interacting with Two-Polypeptide Chiral Liquid Crystalline Solvents by Natural Abundance Deuterium (NAD) NMR. J Phys Chem A 2016; 120:6076-88. [DOI: 10.1021/acs.jpca.6b04254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zeinab Serhan
- RMN en
Milieu Orienté,
ICMMO, UMR CNRS 8182, Université de Paris Sud/Université Paris-Saclay, Bât. 410, F-91405 Orsay cedex, France
| | - Christie Aroulanda
- RMN en
Milieu Orienté,
ICMMO, UMR CNRS 8182, Université de Paris Sud/Université Paris-Saclay, Bât. 410, F-91405 Orsay cedex, France
| | - Philippe Lesot
- RMN en
Milieu Orienté,
ICMMO, UMR CNRS 8182, Université de Paris Sud/Université Paris-Saclay, Bât. 410, F-91405 Orsay cedex, France
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