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Sobornova VV, Belov KV, Krestyaninov MA, Khodov IA. Influence of Solvent Polarity on the Conformer Ratio of Bicalutamide in Saturated Solutions: Insights from NOESY NMR Analysis and Quantum-Chemical Calculations. Int J Mol Sci 2024; 25:8254. [PMID: 39125824 PMCID: PMC11311660 DOI: 10.3390/ijms25158254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The study presents a thorough and detailed analysis of bicalutamide's structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into 'closed' and 'open' types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of 'closed' conformers in non-polar solvents and a significant presence of 'open' conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment's impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development.
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Affiliation(s)
| | | | | | - Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
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2
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Alegre‐Requena JV, Sowndarya S. V. S, Pérez‐Soto R, Alturaifi TM, Paton RS. AQME: Automated quantum mechanical environments for researchers and educators. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- Juan V. Alegre‐Requena
- Dpto. de Química Inorgánica Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC‐Universidad de Zaragoza Zaragoza Spain
| | | | - Raúl Pérez‐Soto
- Department of Chemistry Colorado State University Fort Collins Colorado USA
| | - Turki M. Alturaifi
- Department of Chemistry Colorado State University Fort Collins Colorado USA
| | - Robert S. Paton
- Department of Chemistry Colorado State University Fort Collins Colorado USA
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3
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Structures Controlled by Entropy: The Flexibility of Strychnine as Example. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227987. [PMID: 36432085 PMCID: PMC9692940 DOI: 10.3390/molecules27227987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term TΔS of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and 3JHH couplings as well.
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4
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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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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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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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Navarro-Vázquez A, Gil RR, Blinov K. Computer-Assisted 3D Structure Elucidation (CASE-3D) of Natural Products Combining Isotropic and Anisotropic NMR Parameters. JOURNAL OF NATURAL PRODUCTS 2018; 81:203-210. [PMID: 29323895 DOI: 10.1021/acs.jnatprod.7b00926] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A computer-assisted structural elucidation (CASE-3D) strategy based on the use of isotropic and/or anisotropic NMR data is proposed to elucidate relative configuration and preferred conformation in complex natural products. The methodology involves the selection of conformational models through the use of the Akaike Information Criterion and scoring of the different configurations. As illustrative examples, the methodology furnished the correct configuration of the already known compounds artemisinin (1) and homodimericin A (2). Revised structures (5 and 6), including their absolute configuration, for the recently reported curcusones I (3) and J (4) are proposed.
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Affiliation(s)
- Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco , Avenida Professor Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Kirill Blinov
- MestReLab Research S. L. Feliciano Barrera , 9 Baixo, Santiago de Compostela, A Coruña, 15706 Spain
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Powell J, Valenti D, Bobnar H, Drain E, Elliott B, Frank S, McCullough T, Moore S, Kettring A, Iuliucci R, Harper JK. Evaluating the accuracy of theoretical one-bond 13 C─ 13 C scalar couplings and their ability to predict structure in a natural product. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:979-989. [PMID: 28557141 DOI: 10.1002/mrc.4616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
This study explores the feasibility of using a combination of experimental and theoretical 1-bond 13 C─13 C scalar couplings (1 JCC ) to establish structure in organic compounds, including unknowns. Historically, n JCC and n JCH studies have emphasized 2 and 3-bond couplings, yet 1 JCC couplings exhibit significantly larger variations. Moreover, recent improvements in experimental measurement and data processing methods have made 1 JCC data more available. Herein, an approach is evaluated in which a collection of theoretical structures is created from a partial nuclear magnetic resonance structural characterization. Computed 1 JCC values are compared to experimental data to identify candidates giving the best agreement. This process requires knowledge of the error in theoretical methods, thus the B3LYP, B3PW91, and PBE0 functionals are evaluated by comparing to 27 experimental values from INADEQUATE. Respective errors of ±1.2, ±3.8, and ±2.3 Hz are observed. An initial test of this methodology involves the natural product 5-methylmellein. In this case, only a single candidate matches experimental data with high statistical confidence. This analysis establishes the intramolecular hydrogen-bonding arrangement, ring heteroatom identity, and conformation at one position. This approach is then extended to hydroheptelidic acid, a natural product not fully characterized in prior studies. The experimental/theoretical approach proposed herein identifies a single best-fit structure from among 26 candidates and establishes, for the first time, 1 configuration and 3 conformations to complete the characterization. These results suggest that accurate and complete structural characterizations of many moderately sized organic structures (<800 Da) may be possible using only 1 JCC data.
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Affiliation(s)
- Jacob Powell
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Domenic Valenti
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Harley Bobnar
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Erika Drain
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Blaine Elliott
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sydney Frank
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Tyler McCullough
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sean Moore
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Andrew Kettring
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Robbie Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - James K Harper
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
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Kaltschnee L, Knoll K, Schmidts V, Adams RW, Nilsson M, Morris GA, Thiele CM. Extraction of distance restraints from pure shift NOE experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 271:99-109. [PMID: 27591956 DOI: 10.1016/j.jmr.2016.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
NMR techniques incorporating pure shift methods to improve signal resolution have recently attracted much attention, owing to their potential use in studies of increasingly complex molecular systems. Extraction of frequencies from these simplified spectra enables easier structure determination, but only a few of the methods presented provide structural parameters derived from signal integral measurements. In particular, for quantification of the nuclear Overhauser effect (NOE) it is highly desirable to utilize pure shift techniques where signal overlap normally prevents accurate signal integration, to enable measurement of a larger number of interatomic distances. However, robust methods for the measurement of interatomic distances using the recently developed pure shift techniques have not been reported to date. In this work we discuss some of the factors determining the accuracy of measurements of signal integrals in interferogram-based Zangger-Sterk (ZS) pure shift NMR experiments. The ZS broadband homodecoupling technique is used in different experiments designed for quantitative NOE determination from pure shift spectra. It is shown that the techniques studied can be used for quantitative extraction of NOE-derived distance restraints, as exemplified for the test case of strychnine.
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Affiliation(s)
- Lukas Kaltschnee
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany
| | - Kevin Knoll
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany
| | - Ralph W Adams
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Mathias Nilsson
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Gareth A Morris
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany.
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Thiele CM, Kolmer A. Response to "Comment on "Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone" by I.A. Khodov, M.G. Kiselev, V.V. Klochkov, S.V. Efimov [http://dx.doi.org/10.1016/j.jmr.2016.02.009]" - Or Life is about compromises. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 266:69-72. [PMID: 26947752 DOI: 10.1016/j.jmr.2016.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
| | - Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
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Reinscheid F, Schmidt M, Abromeit H, Liening S, Scriba G, Reinscheid U. Structural and chiroptical analysis of naturally occurring (–)-strychnine. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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12
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Reinscheid F, Reinscheid U. Stereochemical analysis of (+)-limonene using theoretical and experimental NMR and chiroptical data. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Reinscheid F, Reinscheid U. Stereochemical analysis of menthol and menthylamine isomers using calculated and experimental optical rotation data. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kolmer A, Edwards LJ, Kuprov I, Thiele CM. Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 261:101-109. [PMID: 26556179 DOI: 10.1016/j.jmr.2015.10.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
To understand the properties and/or reactivity of an organic molecule, an understanding of its three-dimensional structure is necessary. Simultaneous determination of configuration and conformation often poses a daunting challenge. Thus, the more information accessible for a given molecule, the better. Additionally to (3)J-couplings, two sources of information, quantitative NOE and more recently also RDCs, are used for conformational analysis by NMR spectroscopy. In this paper, we compare these sources of conformational information in two molecules: the configurationally well-characterized strychnine 1, and the only recently configurationally and conformationally characterized α-methylene-γ-butyrolactone 2. We discuss possible sources of error in the measurement and analysis process, and how to exclude them. By this means, we are able to bolster the previously proposed flexibility for these two molecules.
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Affiliation(s)
- Andreas Kolmer
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany
| | - Luke J Edwards
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QG, United Kingdom
| | - Ilya Kuprov
- School of Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, University Road, Southampton SO17 1BJ, United Kingdom
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, 64287 Darmstadt, Germany.
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