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Interrogating the configurational stability of atropisomers

Nature Protocols volume 18, pages 2745–2771 (2023)Cite this article

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Abstract

Atropisomers are molecules whose stereogenicity arises from restricted rotation about a single bond. They are of current importance because of their applications in catalysis, medicine and materials science. The defining feature of atropisomeric molecules is that their stereoisomers are related to one another by bond rotation: as a result, evaluating their configurational stability (i.e., the rate at which their stereoisomers interconvert) is central to any work in this area. Important atropisomeric scaffolds include C–C linked biaryls, such as the ligand BINAP and the drug vancomycin, and C–N linked amine derivatives such as the drug telenzepine. This article focuses on the three most widely used experimental methods that are available to measure the rate of racemization in atropisomers, namely: (i) kinetic analysis of the racemization of an enantioenriched sample, (ii) dynamic HPLC and (iii) variable-temperature NMR. For each technique, an explanation of the theory is set out, followed by a detailed experimental procedure. A discussion is also included of which technique to try when confronted with a new molecular structure whose properties are not yet known. None of the three procedures require complex experimental techniques, and all can be performed by using standard analytical equipment (NMR and HPLC). The time taken to determine a racemization rate depends on which experimental method is required, but for a new compound it is generally possible to measure a racemization rate in <1 d.

Key points

  • Stereoisomers of atropisomeric molecules interconvert by rotation of a single bond. If the interconversion rate is slow enough, the atropisomers can be separated by HPLC. After enrichment of one isomer, the kinetics of racemization can be determined.

  • At increasing rates of interconversion, analytical HPLC shows two peaks, a ‘Batman’ profile (dynamic HPLC) or a single peak.

  • For molecules with faster interconversion, variable-temperature NMR can be performed.

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Fig. 1: An overview of atropisomerism and configurational stability.
Fig. 2: Different timescales for bond rotation and definitions of atropisomerism.
Fig. 3: Kinetic analysis of the racemization of an enantioenriched sample.
Fig. 4: Representative example.
Fig. 5: Dynamic HPLC and calculations using the unified equation.
Fig. 6: Representative example.
Fig. 7: Schematic example of an axially chiral biaryl.
Fig. 8: Representative example.
Fig. 9: Workplan for analyzing the barrier of a completely unknown compound.
Fig. 10: Analytical HPLC data for illustrative compound 1.
Fig. 11: Semi-preparative HPLC isolation of a single enantiomer.
Fig. 12: Monitoring atropisomer racemization by HPLC at elevated temperature.
Fig. 13: Using ΔG‡ to estimate racemization rates at other temperatures by using the ‘Eyring equation calculator’.
Fig. 14: Analytical HPLC data for illustrative compound rac-2.
Fig. 15: Analytical HPLC data for illustrative compound rac-2.
Fig. 16: 1H NMR spectrum of 4 at 20 °C in d8-toluene.
Fig. 17: 1H VT-NMR spectra of 4 in d8-toluene.
Fig. 18: DNMR in TopSpin.

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Data availability

We have previously reported synthetic procedures and data for compounds 1 (ref. 18), 2 (ref. 11) and 4 (ref. 11), which are used to illustrate all three procedures.

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Acknowledgements

We gratefully acknowledge the EPSRC (EP/S024107/1, EP/R005826/1, EP/L015838/1), ERC (DOGMATRON AdG 883786) and Royal Society (RGS\R1\221162) for financial support.

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Authors and Affiliations

  1. School of Chemistry, University of Bristol, Bristol, UK

    Jean-Paul Heeb & Jonathan Clayden

  2. Chemistry Research Laboratory, University of Oxford, Oxford, UK

    Martin D. Smith

  3. School of Natural and Environmental Sciences (Chemistry), Newcastle University, Newcastle Upon Tyne, UK

    Roly J. Armstrong

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The manuscript was jointly conceived and written through the contributions of all authors.

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Correspondence to Jonathan Clayden, Martin D. Smith or Roly J. Armstrong.

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Nature Protocols thanks Zhenhua Gu, Osamu Kitagawa and Bingfeng Shi for their contribution to the peer review of this work.

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Key references using this protocol

Costil, R. et al. J. Angew. Chem. Int. Ed. Engl. 59, 18670–18678 (2020): https://doi.org/10.1002/anie.202007595

Staniland, S. et al. Angew. Chem. Int. Ed. Engl. 55, 10755–10759 (2016): https://doi.org/10.1002/anie.201605486

Jolliffe, J. D. et al. Nat. Chem. 9, 558–562 (2017): https://doi.org/10.1038/nchem.2710

Armstrong, R. J. & Smith, M. D. Angew. Chem. Int. Ed. Engl. 53, 12822–12826 (2014): https://doi.org/10.1002/anie.201408205

Surgenor, R. R. et al. Nat. Chem. 15, 357–365 (2023): https://doi.org/10.1038/s41557-022-01095-9

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Heeb, JP., Clayden, J., Smith, M.D. et al. Interrogating the configurational stability of atropisomers. Nat Protoc 18, 2745–2771 (2023). https://doi.org/10.1038/s41596-023-00859-y

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