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Artificial molecular pumps

Nature Reviews Methods Primers volume 4, Article number: 13 (2024) Cite this article

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Abstract

Reflecting on recent progress in bottom-up engineering focused on creating the smallest devices capable of controlling nanoscale motion, artificial molecular pumps (AMPs) are among some of the most highly studied wholly synthetic machines. In addition to exploring their applications in synthesizing mechanically bonded compounds, including polymers and materials, the design features and underlying fundamental physical principles of rotaxane-based AMPs are discussed in this Primer. Current limitations in AMP design are reviewed, and potential strategies to overcome these limitations are evaluated. Anticipated future developments in this rapidly evolving area of science are considered. Although still in their infancy, the design and synthesis of AMPs have already led to new insights into fundamental molecular principles, such as kinetic asymmetry, trajectory thermodynamics and the non-equilibrium pumping equality. With the ineluctable continuing development of AMPs, an increasing number of ground-breaking discoveries are anticipated in the physical and life sciences.

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Fig. 1: Physical principles of artificial molecular pumps.
Fig. 2: Unidirectional molecular transport.
Fig. 3: Redox-driven AMP.
Fig. 4: Chemical pulse-driven and catalysis-driven AMPs.
Fig. 5: Utilizing molecular pumps for the syntheses of mechanically interlocked molecules.
Fig. 6: Utilizing molecular pumps for the syntheses of mechanically interlocked polyrotaxanes.
Fig. 7: Active mechanisorption driven by pumping cassettes.

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References

  1. Astumian, R. D. Microscopic reversibility as the organizing principle of molecular machines. Nat. Nanotechnol. 7, 684–688 (2012).

    Article  ADS  CAS  PubMed  Google Scholar 

  2. Boyer, P. D. Energy, life, and ATP (Nobel lecture). Angew. Chem. Int. Ed. 37, 2296–2307 (1998).

    Article  Google Scholar 

  3. Skou, J. C. The identification of the sodium–potassium pump (Nobel lecture). Angew. Chem. Int. Ed. 37, 2320–2328 (1998).

    Article  CAS  Google Scholar 

  4. Walker, J. E. ATP synthesis by rotary catalysis (Nobel lecture). Angew. Chem. Int. Ed. 37, 2308–2319 (1998).

    Article  CAS  Google Scholar 

  5. Lanyi, J. K. & Pohorille, A. Proton pumps: mechanism of action and applications. Trends Biotechnol. 19, 140–144 (2001).

    Article  CAS  PubMed  Google Scholar 

  6. Gouaux, E. & MacKinnon, R. Principles of selective ion transport in channels and pumps. Science 310, 1461–1465 (2005).

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Balzani, V., Credi, A., Raymo, F. M. & Stoddart, J. F. Artificial molecular machines. Angew. Chem. Int. Ed. 39, 3348–3391 (2000).

    Article  ADS  CAS  Google Scholar 

  8. Browne, W. R. & Feringa, B. L. Making molecular machines work. Nat. Nanotechnol. 1, 25–35 (2006).

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Erbas-Cakmak, S., Leigh, D. A., McTernan, C. T. & Nussbaumer, A. L. Artificial molecular machines. Chem. Rev. 115, 10081–10206 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kay, E. R. & Leigh, D. A. Rise of the molecular machines. Angew. Chem. Int. Ed. 54, 10080–10088 (2015).

    Article  CAS  Google Scholar 

  11. Cheng, C. & Stoddart, J. F. Wholly synthetic molecular machines. ChemPhysChem 17, 1780–1793 (2016).

    Article  CAS  PubMed  Google Scholar 

  12. Sauvage, J.-P. From chemical topology to molecular machines (Nobel lecture). Angew. Chem. Int. Ed. 56, 11080–11093 (2017).

    Article  CAS  Google Scholar 

  13. Stoddart, J. F. Mechanically interlocked molecules (MIMs) — molecular shuttles, switches, and machines (Nobel lecture). Angew. Chem. Int. Ed. 56, 11094–11125 (2017).

    Article  CAS  Google Scholar 

  14. Feringa, B. L. The art of building small: from molecular switches to motors (Nobel lecture). Angew. Chem. Int. Ed. 56, 11060–11078 (2017).

    Article  CAS  Google Scholar 

  15. Aprahamian, I. The future of molecular machines. ACS Cent. Sci. 6, 347–358 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Bruns, C. J. Moving forward in the semantic soup of artificial molecular machine taxonomy. Nat. Nanotechnol. 17, 1231–1234 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  17. Stoddart, J. F. The chemistry of the mechanical bond. Chem. Soc. Rev. 38, 1802–1820 (2009).

    Article  CAS  PubMed  Google Scholar 

  18. Bruns, C. J. & Stoddart, J. F. The Nature of the Mechanical Bond: From Molecules to Machines (Wiley, 2016). This book features the chemistry of the mechanical bond and its applications in the construction of artificial molecular machines.

  19. Sluysmans, D. & Stoddart, J. F. The burgeoning of mechanically interlocked molecules in chemistry. Trends Chem. 1, 185–197 (2019).

    Article  CAS  Google Scholar 

  20. Ashton, P. R. et al. Rotaxane or pseudorotaxane? That is the question! J. Am. Chem. Soc. 120, 2297–2307 (1998).

    Article  CAS  Google Scholar 

  21. Bruns, C. J. & Stoddart, J. F. Rotaxane-based molecular muscles. Acc. Chem. Res. 47, 2186–2199 (2014).

    Article  CAS  PubMed  Google Scholar 

  22. Leigh, D. A., Wong, J. K. Y., Dehez, F. & Zerbetto, F. Unidirectional rotation in a mechanically interlocked molecular rotor. Nature 424, 174–179 (2003).

    Article  ADS  CAS  PubMed  Google Scholar 

  23. Hernández, J. V., Kay, E. R. & Leigh, D. A. A reversible synthetic rotary molecular motor. Science 306, 1532–1537 (2004).

    Article  ADS  PubMed  Google Scholar 

  24. Gil-Ramírez, G., Leigh, D. A. & Stephens, A. J. Catenanes: fifty years of molecular links. Angew. Chem. Int. Ed. 54, 6110–6150 (2015).

    Article  Google Scholar 

  25. Stoddart, J. F. Putting mechanically interlocked molecules (MIMs) to work in tomorrow’s world. Angew. Chem. Int. Ed. 53, 11102–11104 (2014).

    Article  CAS  Google Scholar 

  26. Heard, A. W. & Goldup, S. M. Simplicity in the design, operation, and applications of mechanically interlocked molecular machines. ACS Cent. Sci. 6, 117–128 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Anelli, P. L., Spencer, N. & Stoddart, J. F. A molecular shuttle. J. Am. Chem. Soc. 113, 5131–5133 (1991). It was in this communication that it was claimed that the technology for building “molecular machines” would emerge.

    Article  CAS  PubMed  Google Scholar 

  28. Murakami, H., Kawabuchi, A., Kotoo, K., Kunitake, M. & Nakashima, N. A light-driven molecular shuttle based on a rotaxane. J. Am. Chem. Soc. 119, 7605–7606 (1997).

    Article  CAS  Google Scholar 

  29. Silvi, S., Venturi, M. & Credi, A. Artificial molecular shuttles: from concepts to devices. J. Mater. Chem. 19, 2279–2294 (2009).

    Article  CAS  Google Scholar 

  30. Chen, S. et al. An artificial molecular shuttle operates in lipid bilayers for ion transport. J. Am. Chem. Soc. 140, 17992–17998 (2018).

    Article  CAS  PubMed  Google Scholar 

  31. Bissell, R. A., Córdova, E., Kaifer, A. E. & Stoddart, J. F. A chemically and electrochemically switchable molecular shuttle. Nature 369, 133–137 (1994).

    Article  ADS  CAS  Google Scholar 

  32. Asakawa, M. et al. A chemically and electrochemically switchable [2]catenane incorporating a tetrathiafulvalene unit. Angew. Chem. Int. Ed. 37, 333–337 (1998).

    Article  CAS  Google Scholar 

  33. Chatterjee, M. N., Kay, E. R. & Leigh, D. A. Beyond switches: ratcheting a particle energetically uphill with a compartmentalized molecular machine. J. Am. Chem. Soc. 128, 4058–4073 (2006).

    Article  CAS  PubMed  Google Scholar 

  34. Dattler, D. et al. Design of collective motions from synthetic molecular switches, rotors, and motors. Chem. Rev. 120, 310–433 (2020).

    Article  CAS  PubMed  Google Scholar 

  35. Kay, E. R., Leigh, D. A. & Zerbetto, F. Synthetic molecular motors and mechanical machines. Angew. Chem. Int. Ed. 46, 72–191 (2007).

    Article  ADS  CAS  Google Scholar 

  36. Wilson, M. R. et al. An autonomous chemically fuelled small-molecule motor. Nature 534, 235–240 (2016). To our knowledge, this article reports the first autonomous chemically fuelled molecular rotary motor.

    Article  ADS  CAS  PubMed  Google Scholar 

  37. Kassem, S. et al. Artificial molecular motors. Chem. Soc. Rev. 46, 2592–2621 (2017).

    Article  CAS  PubMed  Google Scholar 

  38. Iino, R., Kinbara, K. & Bryant, Z. Introduction: molecular motors. Chem. Rev. 120, 1–4 (2020).

    Article  CAS  PubMed  Google Scholar 

  39. Baroncini, M., Silvi, S. & Credi, A. Photo- and redox-driven artificial molecular motors. Chem. Rev. 120, 200–268 (2020). This review summarizes recent developments in photodriven and redox-driven artificial molecular motors.

    Article  CAS  PubMed  Google Scholar 

  40. Zhang, L. et al. An electric molecular motor. Nature 613, 280–286 (2023). To our knowledge, this paper reports the first example of a catenane-based electric molecular motor.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  41. Cheng, C. et al. An artificial molecular pump. Nat. Nanotechnol. 10, 547–553 (2015). To our knowledge, this paper reports the first example of an artificial molecular pump.

    Article  ADS  CAS  PubMed  Google Scholar 

  42. Qiu, Y., Feng, Y., Guo, Q.-H., Astumian, R. D. & Stoddart, J. F. Pumps through the ages. Chem 6, 1952–1977 (2020). This article provides an overview of recent advances towards the design and synthesis of AMPs.

    Article  CAS  Google Scholar 

  43. Feng, Y. et al. Molecular pumps and motors. J. Am. Chem. Soc. 143, 5569–5591 (2021).

    Article  CAS  PubMed  Google Scholar 

  44. Seale, J. S. W., Feng, Y., Feng, L., Astumian, R. D. & Stoddart, J. F. Polyrotaxanes and the pump paradigm. Chem. Soc. Rev. 51, 8450–8475 (2022).

    Article  CAS  PubMed  Google Scholar 

  45. Abendroth, J. M., Bushuyev, O. S., Weiss, P. S. & Barrett, C. J. Controlling motion at the nanoscale: rise of the molecular machines. ACS Nano 9, 7746–7768 (2015).

    Article  CAS  PubMed  Google Scholar 

  46. Astumian, R. D. Design principles for Brownian molecular machines: how to swim in molasses and walk in a hurricane. Phys. Chem. Chem. Phys. 9, 5067–5083 (2007).

    Article  CAS  PubMed  Google Scholar 

  47. Cheng, C., McGonigal, P. R., Stoddart, J. F. & Astumian, R. D. Design and synthesis of nonequilibrium systems. ACS Nano 9, 8672–8688 (2015). The review summarizes the progress in making the first AMPs and outlines a theoretical framework for linking the autonomous operation of the pumps to the catalysis of a chemical reaction.

    Article  CAS  PubMed  Google Scholar 

  48. Baroncini, M. et al. Making and operating molecular machines: a multidisciplinary challenge. ChemistryOpen 7, 169–179 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Müller-Dethlefs, K. & Hobza, P. Noncovalent interactions: a challenge for experiment and theory. Chem. Rev. 100, 143–168 (2000).

    Article  PubMed  Google Scholar 

  50. Laidler, K. J. Chemical Kinetics 2nd edn (McGraw-Hill, 1965).

  51. Astumian, R. D. Kinetic asymmetry allows macromolecular catalysts to drive an information ratchet. Nat. Commun. 10, 3837 (2019). This article explains that under non-equilibrium conditions a system’s state is influenced by kinetics as well as by thermodynamics.

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  52. Corra, S. et al. Kinetic and energetic insights into the dissipative non-equilibrium operation of an autonomous light-powered supramolecular pump. Nat. Nanotechnol. 17, 746–751 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  53. Mandal, N. S., Sen, A. & Astumian, R. D. Kinetic asymmetry versus dissipation in the evolution of chemical systems as exemplified by single enzyme chemotaxis. J. Am. Chem. Soc. 145, 5730–5738 (2023).

    Article  CAS  PubMed  Google Scholar 

  54. Persch, E., Dumele, O. & Diederich, F. Molecular recognition in chemical and biological systems. Angew. Chem. Int. Ed. 54, 3290–3327 (2015).

    Article  CAS  Google Scholar 

  55. Bott, G., Field, L. D. & Sternhell, S. Steric effects. A study of a rationally designed system. J. Am. Chem. Soc. 102, 5618–5626 (1980).

    Article  CAS  Google Scholar 

  56. Ragazzon, G., Baroncini, M., Silvi, S., Venturi, M. & Credi, A. Light-powered autonomous and directional molecular motion of a dissipative self-assembling system. Nat. Nanotechnol. 10, 70–75 (2015). To our knowledge, this article reports the first example of an autonomous unidirectional molecular transport powered by light.

    Article  ADS  CAS  PubMed  Google Scholar 

  57. Corra, S., Curcio, M., Baroncini, M., Silvi, S. & Credi, A. Photoactivated artificial molecular machines that can perform tasks. Adv. Mater. 32, e1906064 (2020).

    Article  PubMed  Google Scholar 

  58. García-López, V., Liu, D. & Tour, J. M. Light-activated organic molecular motors and their applications. Chem. Rev. 120, 79–124 (2020).

    Article  PubMed  Google Scholar 

  59. Corra, S. et al. Artificial supramolecular pumps powered by light. Chem. Eur. J. 27, 11076–11083 (2021).

    Article  CAS  PubMed  Google Scholar 

  60. Pooler, D. R. S., Lubbe, A. S., Crespi, S. & Feringa, B. L. Designing light-driven rotary molecular motors. Chem. Sci. 12, 14964–14986 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Gingrich, T. R. Measuring how effectively light drives a molecular pump. Nat. Nanotechnol. 17, 675–676 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  62. Amano, S., Borsley, S., Leigh, D. A. & Sun, Z. Chemical engines: driving systems away from equilibrium through catalyst reaction cycles. Nat. Nanotechnol. 16, 1057–1067 (2021).

    Article  ADS  CAS  PubMed  Google Scholar 

  63. Mondal, A., Toyoda, R., Costil, R. & Feringa, B. L. Chemically driven rotatory molecular machines. Angew. Chem. Int. Ed. 61, e202206631 (2022).

    Article  ADS  CAS  Google Scholar 

  64. Borsley, S., Leigh, D. A. & Roberts, B. M. W. Chemical fuels for molecular machinery. Nat. Chem. 14, 728–738 (2022).

    Article  CAS  PubMed  Google Scholar 

  65. Trabolsi, A. et al. Radically enhanced molecular recognition. Nat. Chem. 2, 42–49 (2010). To our knowledge, this research demonstrates, for the first time, that the dimerization of radical cations can be harnessed to control motion in molecular machines.

    Article  CAS  PubMed  Google Scholar 

  66. Jiao, Y. et al. Electron-catalysed molecular recognition. Nature 603, 265–270 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  67. Lau, B., Kedem, O., Schwabacher, J., Kwasnieski, D. & Weiss, E. A. An introduction to ratchets in chemistry and biology. Mater. Horiz. 4, 310–318 (2017).

    Article  CAS  Google Scholar 

  68. Astumian, R. D. & Derényi, I. Fluctuation driven transport and models of molecular motors and pumps. Eur. Biophys. J. 27, 474–489 (1998). This article introduces the distinction between energy and information ratchets.

    Article  CAS  PubMed  Google Scholar 

  69. Astumian, R. D. et al. Non-equilibrium kinetics and trajectory thermodynamics of synthetic molecular pumps. Mater. Chem. Front. 4, 1304–1314 (2020).

    Article  CAS  Google Scholar 

  70. Crowley, J. D., Goldup, S. M., Lee, A.-L., Leigh, D. A. & McBurney, R. T. Active metal template synthesis of rotaxanes, catenanes and molecular shuttles. Chem. Soc. Rev. 38, 1530–1541 (2009).

    Article  CAS  PubMed  Google Scholar 

  71. Li, H. et al. Mechanical bond formation by radical templation. Angew. Chem. Int. Ed. 49, 8260–8265 (2010).

    Article  ADS  CAS  Google Scholar 

  72. Qu, D.-H. & Tian, H. Novel and efficient templates for assembly of rotaxanes and catenanes. Chem. Sci. 2, 1011–1015 (2011).

    Article  CAS  Google Scholar 

  73. Evans, N. H. & Beer, P. D. Progress in the synthesis and exploitation of catenanes since the millennium. Chem. Soc. Rev. 43, 4658–4683 (2014).

    Article  CAS  PubMed  Google Scholar 

  74. Feng, L. et al. Active mechanisorption driven by pumping cassettes. Science 374, 1215–1221 (2021). To our knowledge, this study presents the first example of active adsorption onto the surface of a 2D MOF that is realized during molecular pumping.

    Article  ADS  CAS  PubMed  Google Scholar 

  75. Yoshino, N., Satake, A. & Kobuke, Y. An artificial ion channel formed by a macrocyclic resorcin[4]arene with amphiphilic cholic acid ether groups. Angew. Chem. Int. Ed. 40, 457–459 (2001).

    Article  CAS  Google Scholar 

  76. Bennett, I. M. et al. Active transport of Ca2+ by an artificial photosynthetic membrane. Nature 420, 398–401 (2002).

    Article  ADS  CAS  PubMed  Google Scholar 

  77. Langton, M. J. Engineering of stimuli-responsive lipid-bilayer membranes using supramolecular systems. Nat. Rev. Chem. 5, 46–61 (2021).

    Article  CAS  PubMed  Google Scholar 

  78. Li, H. et al. Relative unidirectional translation in an artificial molecular assembly fueled by light. J. Am. Chem. Soc. 135, 18609–18620 (2013). To our knowledge, this article describes the first example of redox-driven unidirectional molecular transport.

    Article  CAS  PubMed  Google Scholar 

  79. Meng, Z., Xiang, J.-F. & Chen, C.-F. Directional molecular transportation based on a catalytic stopper-leaving rotaxane system. J. Am. Chem. Soc. 138, 5652–5658 (2016).

    Article  CAS  PubMed  Google Scholar 

  80. Erbas-Cakmak, S. et al. Rotary and linear molecular motors driven by pulses of a chemical fuel. Science 358, 340–343 (2017). This article reports the design and synthesis of chemical pulse-driven rotary and linear molecular motors by utilizing an energy ratchet mechanism.

    Article  ADS  CAS  PubMed  Google Scholar 

  81. Pezzato, C. et al. Controlling dual molecular pumps electrochemically. Angew. Chem. Int. Ed. 57, 9325–9329 (2018).

    Article  CAS  Google Scholar 

  82. Qiu, Y. et al. A molecular dual pump. J. Am. Chem. Soc. 141, 17472–17476 (2019).

    Article  CAS  PubMed  Google Scholar 

  83. Guo, Q.-H. et al. Artificial molecular pump operating in response to electricity and light. J. Am. Chem. Soc. 142, 14443–14449 (2020).

    Article  CAS  PubMed  Google Scholar 

  84. Amano, S., Fielden, S. D. P. & Leigh, D. A. A catalysis-driven artificial molecular pump. Nature 594, 529–534 (2021). To our knowledge, this article reports the first autonomous catalysis-driven (chemically fuelled) molecular pump.

    Article  ADS  CAS  PubMed  Google Scholar 

  85. Astumian, R. D. Thermodynamics and kinetics of a Brownian motor. Science 276, 917–922 (1997).

    Article  CAS  PubMed  Google Scholar 

  86. Astumian, R. D. & Bier, M. Mechanochemical coupling of the motion of molecular motors to ATP hydrolysis. Biophys. J. 70, 637–653 (1996).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  87. Baroncini, M., Silvi, S., Venturi, M. & Credi, A. Photoactivated directionally controlled transit of a non-symmetric molecular axle through a macrocycle. Angew. Chem. Int. Ed. 51, 4223–4226 (2012).

    Article  CAS  Google Scholar 

  88. Zhou, H.-Y., Han, Y., Shi, Q. & Chen, C.-F. Directional transportation of a helic[6]arene along a nonsymmetric molecular axle. J. Org. Chem. 84, 5872–5876 (2019).

    Article  CAS  PubMed  Google Scholar 

  89. Canton, M. et al. Second-generation light-fueled supramolecular pump. J. Am. Chem. Soc. 143, 10890–10894 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. David, A. H. G., García–Cerezo, P., Campaña, A. G., Santoyo–González, F. & Blanco, V. Vinyl sulfonyl chemistry-driven unidirectional transport of a macrocycle through a [2]rotaxane. Org. Chem. Front. 9, 633–642 (2022).

    Article  CAS  Google Scholar 

  91. Cheng, C. Y. et al. Energetically demanding transport in a supramolecular assembly. J. Am. Chem. Soc. 136, 14702–14705 (2014).

    Article  CAS  PubMed  Google Scholar 

  92. Odell, B. et al. Cyclobis(paraquat-p-phenylene). A tetracationic multipurpose receptor. Angew. Chem. Int. Ed. Engl. 27, 1547–1550 (1988).

    Article  Google Scholar 

  93. Goodnow, T. T., Reddington, M. V., Stoddart, J. F. & Kaifer, A. E. Cyclobis(paraquat-p-phenylene): a novel synthetic receptor for amino acids with electron-rich aromatic moieties. J. Am. Chem. Soc. 113, 4335–4337 (1991).

    Article  CAS  Google Scholar 

  94. Chen, X.-Y., Chen, H. & Stoddart, J. F. The story of the little blue box: a tribute to Siegfried Hünig. Angew. Chem. Int. Ed. 62, e202211387 (2023).

    Article  CAS  Google Scholar 

  95. Gutmann, V. The Donor-Acceptor Approach to Molecular Interactions (Springer, 1978).

  96. Mandal, A. K., Gangopadhyay, M. & Das, A. Photo-responsive pseudorotaxanes and assemblies. Chem. Soc. Rev. 44, 663–676 (2015).

    Article  CAS  PubMed  Google Scholar 

  97. Ashton, P. R. et al. Dialkylammonium ion/crown ether complexes: the forerunners of a new family of interlocked molecules. Angew. Chem. Int. Ed. Engl. 34, 1865–1869 (1995).

    Article  CAS  Google Scholar 

  98. Bandara, H. M. D. & Burdette, S. C. Photoisomerization in different classes of azobenzene. Chem. Soc. Rev. 41, 1809–1825 (2012).

    Article  CAS  PubMed  Google Scholar 

  99. Cai, K., Zhang, L., Astumian, R. D. & Stoddart, J. F. Radical-pairing-induced molecular assembly and motion. Nat. Rev. Chem. 5, 447–465 (2021).

    Article  CAS  PubMed  Google Scholar 

  100. Pezzato, C. et al. An efficient artificial molecular pump. Tetrahedron 73, 4849–4857 (2017).

    Article  CAS  Google Scholar 

  101. Qiu, Y. et al. A precise polyrotaxane synthesizer. Science 368, 1247–1253 (2020). To our knowledge, this article presents the first example of the use of artificial molecular pumps in the synthesis of poly[n]rotaxanes, featuring precise numbers of rings encircling their polymeric dumbbells.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  102. Li, X. et al. Fluorescence quenching by redox molecular pumping. J. Am. Chem. Soc. 144, 3572–3579 (2022).

    Article  CAS  PubMed  Google Scholar 

  103. McGonigal, P. R. et al. Controlling association kinetics in the formation of donor–acceptor pseudorotaxanes. Tetrahedron Lett. 56, 3591–3594 (2015).

    Article  CAS  Google Scholar 

  104. Pezzato, C., Cheng, C., Stoddart, J. F. & Astumian, R. D. Mastering the non-equilibrium assembly and operation of molecular machines. Chem. Soc. Rev. 46, 5491–5507 (2017). This review summarizes recent developments in non-equilibrium chemistry arising from the application of trajectory thermodynamics and the non-equilibrium pumping equality.

    Article  CAS  PubMed  Google Scholar 

  105. Brown, B. R. The mechanism of thermal decarboxylation. Q. Rev. Chem. Soc. 5, 131–146 (1951).

    Article  CAS  Google Scholar 

  106. Serreli, V., Lee, C.-F., Kay, E. R. & Leigh, D. A. A molecular information ratchet. Nature 445, 523–527 (2007). To our knowledge, this article reports the first example of an artificial molecular machine based on an information ratchet.

    Article  ADS  CAS  PubMed  Google Scholar 

  107. Tian, C., Fielden, S. D. P., Whitehead, G. F. S., Vitorica-Yrezabal, I. J. & Leigh, D. A. Weak functional group interactions revealed through metal-free active template rotaxane synthesis. Nat. Commun. 11, 744 (2020).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  108. Lewis, G. N. & Randall, M. Thermodynamics and the Free Energy of Chemical Substances (McGraw-Hill, 1923).

  109. Lewis, G. N. A new principle of equilibrium. Proc. Natl Acad. Sci. USA 11, 179–183 (1925). This paper introduces the concept of multiple reaction channels for an elementary reaction and also provides a chemical understanding of the principle of microscopic reversibility.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  110. Conyard, J. et al. Ultrafast dynamics in the power stroke of a molecular rotary motor. Nat. Chem. 4, 547–551 (2012).

    Article  CAS  PubMed  Google Scholar 

  111. Blackmond, D. G. “If pigs could fly” chemistry: a tutorial on the principle of microscopic reversibility. Angew. Chem. Int. Ed. 48, 2648–2654 (2009).

    Article  CAS  Google Scholar 

  112. Peliti, L. & Pigolotti, S. Stochastic Thermodynamics: An Introduction (Princeton University Press, 2021).

  113. Koenig, F. O., Horne, F. H. & Mohilner, D. M. On thermodynamic coupling of chemical reactions. J. Am. Chem. Soc. 83, 1029–1033 (1961).

    Article  CAS  Google Scholar 

  114. Astumian, R. D., Chock, P. B., Tsong, T. Y. & Westerhoff, H. V. Effects of oscillations and energy-driven fluctuations on the dynamics of enzyme catalysis and free-energy transduction. Phys. Rev. A 39, 6416–6435 (1989). This article introduces the importance of kinetic asymmetry to control energy usage for performing work in catalytic systems.

    Article  ADS  CAS  Google Scholar 

  115. Astumian, R. D. Thermodynamics and kinetics of molecular motors. Biophys. J. 98, 2401–2409 (2010). This article introduces the seminal discussion of trajectory thermodynamics.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  116. Astumian, R. D. & Robertson, B. Imposed oscillations of kinetic barriers can cause an enzyme to drive a chemical reaction away from equilibrium. J. Am. Chem. Soc. 115, 11063–11068 (1993). This article introduces the non-equilibrium pumping equality.

    Article  CAS  Google Scholar 

  117. Binks, L. et al. The role of kinetic asymmetry and power strokes in an information ratchet. Chem 9, 2902–2917 (2023).

    Article  CAS  Google Scholar 

  118. Astumian, R. D. Nonequilibrium steady states, ratchets, and kinetic asymmetry. Matter 6, 2533–2536 (2023).

    Article  CAS  Google Scholar 

  119. Aprahamian, I. & Goldup, S. M. Non-equilibrium steady states in catalysis, molecular motors, and supramolecular materials: why networks and language matter. J. Am. Chem. Soc. 145, 14169–14183 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Jencks, W. P. How does a calcium pump pump calcium? J. Biol. Chem. 264, 18855–18858 (1989).

    Article  CAS  PubMed  Google Scholar 

  121. Astumian, R. D. Irrelevance of the power stroke for the directionality, stopping force, and optimal efficiency of chemically driven molecular machines. Biophys. J. 108, 291–303 (2015).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  122. Jarzynski, C. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78, 2690–2693 (1997).

    Article  ADS  CAS  Google Scholar 

  123. Mukherjee, S. & Warshel, A. The FoF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function. Photosynth. Res. 134, 1–15 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Astumian, R. D., Mukherjee, S. & Warshel, A. The physics and physical chemistry of molecular machines. ChemPhysChem 17, 1719–1741 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Lancia, F., Ryabchun, A. & Katsonis, N. Life-like motion driven by artificial molecular machines. Nat. Rev. Chem. 3, 536–551 (2019).

    Article  CAS  Google Scholar 

  126. Ren, Y., Jamagne, R., Tetlow, D. J. & Leigh, D. A. A tape-reading molecular ratchet. Nature 612, 78–82 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  127. Han, H., Seale, J. S. W., Feng, L., Qiu, Y. & Stoddart, J. F. Sequence-controlled synthesis of rotaxanes. J. Polym. Sci. 61, 881–902 (2023).

    Article  CAS  Google Scholar 

  128. Binks, L., Tian, C., Fielden, S. D. P., Vitorica-Yrezabal, I. J. & Leigh, D. A. Transamidation-driven molecular pumps. J. Am. Chem. Soc. 144, 15838–15844 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Fuller, A.-M. L., Leigh, D. A. & Lusby, P. J. Sequence isomerism in [3]rotaxanes. J. Am. Chem. Soc. 132, 4954–4959 (2010).

    Article  CAS  PubMed  Google Scholar 

  130. Li, A. et al. Precise control of radial catenane synthesis via clipping and pumping. J. Am. Chem. Soc. 144, 2085–2089 (2022). This article describes the syntheses of a variety of radial catenanes through a so-called clipping-followed-by-pumping strategy.

    Article  CAS  PubMed  Google Scholar 

  131. Nguyen, M. T., Ferris, D. P., Pezzato, C., Wang, Y. & Stoddart, J. F. Densely charged dodecacationic [3]- and tetracosacationic radial [5]catenanes. Chem 4, 2329–2344 (2018).

    Article  CAS  Google Scholar 

  132. Carlone, A., Goldup, S. M., Lebrasseur, N., Leigh, D. A. & Wilson, A. A three-compartment chemically-driven molecular information ratchet. J. Am. Chem. Soc. 134, 8321–8323 (2012).

    Article  CAS  PubMed  Google Scholar 

  133. Grommet, A. B., Feller, M. & Klajn, R. Chemical reactivity under nanoconfinement. Nat. Nanotechnol. 15, 256–271 (2020).

    Article  ADS  CAS  PubMed  Google Scholar 

  134. Berná, J. et al. Macroscopic transport by synthetic molecular machines. Nat. Mater. 4, 704–710 (2005).

    Article  ADS  PubMed  Google Scholar 

  135. Thomas, D. et al. Pumping between phases with a pulsed-fuel molecular ratchet. Nat. Nanotechnol. 17, 701–707 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  136. Fang, L. et al. Mechanically bonded macromolecules. Chem. Soc. Rev. 39, 17–29 (2010).

    Article  CAS  PubMed  Google Scholar 

  137. Mayumi, K., Ito, K. & Kato, K. Polyrotaxane and Slide-Ring Materials (Royal Society of Chemistry, 2016).

  138. Seale, J. S. W., Song, B., Qiu, Y. & Stoddart, J. F. Precise non-equilibrium polypropylene glycol polyrotaxanes. J. Am. Chem. Soc. 144, 16898–16904 (2022).

    Article  CAS  PubMed  Google Scholar 

  139. Ashton, P. R. et al. Supramolecular daisy chains. Angew. Chem. Int. Ed. 37, 1294–1297 (1998).

    Article  CAS  Google Scholar 

  140. Rotzler, J. & Mayor, M. Molecular daisy chains. Chem. Soc. Rev. 42, 44–62 (2013).

    Article  CAS  PubMed  Google Scholar 

  141. Cai, K. et al. Molecular-pump-enabled synthesis of a daisy chain polymer. J. Am. Chem. Soc. 142, 10308–10313 (2020).

    Article  CAS  PubMed  Google Scholar 

  142. Chen, L., Sheng, X., Li, G. & Huang, F. Mechanically interlocked polymers based on rotaxanes. Chem. Soc. Rev. 51, 7046–7065 (2022).

    Article  CAS  PubMed  Google Scholar 

  143. Bruch, L. W. Theory of physisorption interactions. Surf. Sci. 125, 194–217 (1983).

    Article  ADS  CAS  Google Scholar 

  144. Low, M. J. D. Kinetics of chemisorption of gases on solids. Chem. Rev. 60, 267–312 (1960).

    Article  CAS  Google Scholar 

  145. Langmuir, I. Forces near the surfaces of molecules. Chem. Rev. 6, 451–479 (1930).

    Article  Google Scholar 

  146. Lennard-Jones, J. E. Processes of adsorption and diffusion on solid surfaces. Trans. Faraday Soc. 28, 333–359 (1932).

    Article  CAS  Google Scholar 

  147. Furukawa, H., Cordova, K. E., O’Keeffe, M. & Yaghi, O. M. The chemistry and applications of metal-organic frameworks. Science 341, 1230444 (2013).

    Article  PubMed  Google Scholar 

  148. Tannor, D. J. et al. Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory. J. Am. Chem. Soc. 116, 11875–11882 (1994).

    Article  CAS  Google Scholar 

  149. Feller, D. The role of databases in support of computational chemistry calculations. J. Comput. Chem. 17, 1571–1586 (1996).

    Article  CAS  Google Scholar 

  150. Johnson, E. R. et al. Revealing noncovalent interactions. J. Am. Chem. Soc. 132, 6498–6506 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Wang, W.-Z. et al. Light-driven molecular motors boost the selective transport of alkali metal ions through phospholipid bilayers. J. Am. Chem. Soc. 143, 15653–15660 (2021).

    Article  CAS  PubMed  Google Scholar 

  152. Fyles, T. M., Loock, D. & Zhou, X. A voltage-gated ion channel based on a bis-macrocyclic bolaamphiphile. J. Am. Chem. Soc. 120, 2997–3003 (1998).

    Article  CAS  Google Scholar 

  153. Gokel, G. W. & Negin, S. Synthetic ion channels: from pores to biological applications. Acc. Chem. Res. 46, 2824–2833 (2013).

    Article  CAS  PubMed  Google Scholar 

  154. Sakai, N. & Matile, S. Synthetic ion channels. Langmuir 29, 9031–9040 (2013).

    Article  CAS  PubMed  Google Scholar 

  155. Behera, H. & Hou, J.-L. in Handbook of Macrocyclic Supramolecular Assembly (eds Liu, Y., Chen, Y. & Zhang, H.-Y.) 1519–1554 (Springer, 2019).

  156. Sato, K. et al. Supramolecular mechanosensitive potassium channel formed by fluorinated amphiphilic cyclophane. J. Am. Chem. Soc. 144, 11802–11809 (2022).

    Article  CAS  PubMed  Google Scholar 

  157. Zhang, X. & Wang, C. Supramolecular amphiphiles. Chem. Soc. Rev. 40, 94–101 (2011).

    Article  CAS  PubMed  Google Scholar 

  158. Fyles, T. M. How do amphiphiles form ion-conducting channels in membranes? Lessons from linear oligoesters. Acc. Chem. Res. 46, 2847–2855 (2013).

    Article  CAS  PubMed  Google Scholar 

  159. Zhang, X. Supramolecular Amphiphiles (Royal Society of Chemistry, 2017).

  160. Sato, K., Muraoka, T. & Kinbara, K. Supramolecular transmembrane ion channels formed by multiblock amphiphiles. Acc. Chem. Res. 54, 3700–3709 (2021).

    Article  CAS  PubMed  Google Scholar 

  161. Krause, S. & Feringa, B. L. Towards artificial molecular factories from framework-embedded molecular machines. Nat. Rev. Chem. 4, 550–562 (2020).

    Article  CAS  Google Scholar 

  162. Butler, K. T., Davies, D. W., Cartwright, H., Isayev, O. & Walsh, A. Machine learning for molecular and materials science. Nature 559, 547–555 (2018).

    Article  ADS  CAS  PubMed  Google Scholar 

  163. Strieth-Kalthoff, F., Sandfort, F., Segler, M. H. S. & Glorius, F. Machine learning the ropes: principles, applications and directions in synthetic chemistry. Chem. Soc. Rev. 49, 6154–6168 (2020).

    Article  CAS  PubMed  Google Scholar 

  164. Keith, J. A. et al. Combining machine learning and computational chemistry for predictive insights into chemical systems. Chem. Rev. 121, 9816–9872 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Meuwly, M. Machine learning for chemical reactions. Chem. Rev. 121, 10218–10239 (2021).

    Article  CAS  PubMed  Google Scholar 

  166. Bender, A. et al. Evaluation guidelines for machine learning tools in the chemical sciences. Nat. Rev. Chem. 6, 428–442 (2022).

    Article  PubMed  Google Scholar 

  167. Chen, S. et al. Photoactuating artificial muscles of motor amphiphiles as an extracellular matrix mimetic scaffold for mesenchymal stem cells. J. Am. Chem. Soc. 135, 18609–18620 (2013).

    Google Scholar 

  168. Guinart, A. et al. Synthetic molecular motor activates drug delivery from polymersomes. Proc. Natl Acad. Sci. USA 120, e2301279120 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. de Almeida, A. F., Moreira, R. & Rodrigues, T. Synthetic organic chemistry driven by artificial intelligence. Nat. Rev. Chem. 3, 589–604 (2019).

    Article  Google Scholar 

  170. Baum, Z. J. et al. Artificial intelligence in chemistry: current trends and future directions. J. Chem. Inf. Model. 61, 3197–3212 (2021).

    Article  CAS  PubMed  Google Scholar 

  171. Liu, Z., Nalluri, S. K. M. & Stoddart, J. F. Surveying macrocyclic chemistry: from flexible crown ethers to rigid cyclophanes. Chem. Soc. Rev. 46, 2459–2478 (2017).

    Article  CAS  PubMed  Google Scholar 

  172. Gutsche, C. D. Calixarenes. Acc. Chem. Res. 16, 161–170 (1983).

    Article  CAS  Google Scholar 

  173. Crini, G. Review: A history of cyclodextrins. Chem. Rev. 114, 10940–10975 (2014).

    Article  CAS  PubMed  Google Scholar 

  174. Freeman, W. A., Mock, W. L. & Shih, N. Y. Cucurbituril. J. Am. Chem. Soc. 103, 7367–7368 (1981).

    Article  CAS  Google Scholar 

  175. Kim, K. et al. Functionalized cucurbiturils and their applications. Chem. Soc. Rev. 36, 267–279 (2007).

    Article  CAS  PubMed  Google Scholar 

  176. Ogoshi, T., Kanai, S., Fujinami, S., Yamagishi, T.-A. & Nakamoto, Y. para-Bridged symmetrical pillar[5]arenes: their Lewis acid catalyzed synthesis and host–guest property. J. Am. Chem. Soc. 130, 5022–5023 (2008).

    Article  CAS  PubMed  Google Scholar 

  177. Xue, M., Yang, Y., Chi, X., Zhang, Z. & Huang, F. Pillararenes, a new class of macrocycles for supramolecular chemistry. Acc. Chem. Res. 45, 1294–1308 (2012).

    Article  CAS  PubMed  Google Scholar 

  178. Iyoda, M., Yamakawa, J. & Rahman, M. J. Conjugated macrocycles: concepts and applications. Angew. Chem. Int. Ed. 50, 10522–10553 (2011).

    Article  CAS  Google Scholar 

  179. Webber, M. J., Appel, E. A., Meijer, E. W. & Langer, R. Supramolecular biomaterials. Nat. Mater. 15, 13–26 (2016).

    Article  ADS  CAS  PubMed  Google Scholar 

  180. Cui, H. & Xu, B. Supramolecular medicine. Chem. Soc. Rev. 46, 6430–6432 (2017).

    Article  CAS  PubMed  Google Scholar 

  181. Goor, O. J. G. M., Hendrikse, S. I. S., Dankers, P. Y. W. & Meijer, E. W. From supramolecular polymers to multi-component biomaterials. Chem. Soc. Rev. 46, 6621–6637 (2017).

    Article  CAS  PubMed  Google Scholar 

  182. Mogaki, R., Hashim, P. K., Okuro, K. & Aida, T. Guanidinium-based “molecular glues” for modulation of biomolecular functions. Chem. Soc. Rev. 46, 6480–6491 (2017).

    Article  CAS  PubMed  Google Scholar 

  183. Webber, M. J. & Langer, R. Drug delivery by supramolecular design. Chem. Soc. Rev. 46, 6600–6620 (2017).

    Article  CAS  PubMed  Google Scholar 

  184. Sato, K., Hendricks, M. P., Palmer, L. C. & Stupp, S. I. Peptide supramolecular materials for therapeutics. Chem. Soc. Rev. 47, 7539–7551 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Brito, A. et al. Carbohydrate amphiphiles for supramolecular biomaterials: design, self-assembly, and applications. Chem 7, 2943–2964 (2021).

    Article  CAS  Google Scholar 

  186. Zhou, J. et al. Supramolecular cancer nanotheranostics. Chem. Soc. Rev. 50, 2839–2891 (2021).

    Article  CAS  PubMed  Google Scholar 

  187. García-López, V. Molecular machines open cell membranes. Nature 548, 567–572 (2017).

    Article  ADS  PubMed  Google Scholar 

  188. Zhang, Q. et al. Muscle-like artificial molecular actuators for nanoparticles. Chem 4, 2670–2684 (2018).

    Article  CAS  Google Scholar 

  189. Song, Z. et al. Synthetic polypeptides: from polymer design to supramolecular assembly and biomedical application. Chem. Soc. Rev. 46, 6570–6599 (2017).

    Article  CAS  PubMed  Google Scholar 

  190. Moulin, E., Faour, L., Carmona-Vargas, C. C. & Giuseppone, N. From molecular machines to stimuli-responsive materials. Adv. Mater. 32, e1906036 (2020).

    Article  PubMed  Google Scholar 

  191. Xian, S. & Webber, M. J. Temperature-responsive supramolecular hydrogels. J. Mater. Chem. B 8, 9197–9211 (2020).

    Article  CAS  PubMed  Google Scholar 

  192. Cameron, J. M. et al. Supramolecular assemblies of organo-functionalised hybrid polyoxometalates: from functional building blocks to hierarchical nanomaterials. Chem. Soc. Rev. 51, 293–328 (2022).

    Article  CAS  PubMed  Google Scholar 

  193. Ito, K. Slide-ring materials using topological supramolecular architecture. Curr. Opin. Solid State Mater. Sci. 14, 28–34 (2010).

    Article  ADS  CAS  Google Scholar 

  194. Noda, Y., Hayashi, Y. & Ito, K. From topological gels to slide-ring materials. J. Appl. Polym. Sci. 131, 40509 (2014).

    Article  Google Scholar 

  195. Jiang, L. et al. Highly stretchable and instantly recoverable slide-ring gels consisting of enzymatically synthesized polyrotaxane with low host coverage. Chem. Mater. 30, 5013–5019 (2018).

    Article  CAS  Google Scholar 

  196. Choi, S., Kwon, T.-W., Coskun, A. & Choi, J. W. Highly elastic binders integrating polyrotaxanes for silicon microparticle anodes in lithium ion batteries. Science 357, 279–283 (2017).

    Article  ADS  CAS  PubMed  Google Scholar 

  197. Feng, L., Astumian, R. D. & Stoddart, J. F. Controlling dynamics in extended molecular frameworks. Nat. Rev. Chem. 6, 705–725 (2022).

    Article  PubMed  Google Scholar 

  198. Saura-Sanmartin, A. et al. Mechanically interlocked molecules in metal–organic frameworks. Chem. Soc. Rev. 51, 4949–4976 (2022).

    Article  CAS  PubMed  Google Scholar 

  199. Correa, S. et al. Translational applications of hydrogels. Chem. Rev. 121, 11385–11457 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Côté, A. P. et al. Porous, crystalline, covalent organic frameworks. Science 310, 1166–1170 (2005).

    Article  ADS  PubMed  Google Scholar 

  201. Tan, K. T. et al. Covalent organic frameworks. Nat. Rev. Methods Primers 3, 1 (2023).

    Article  CAS  Google Scholar 

  202. Feng, X., Ding, X. & Jiang, D. Covalent organic frameworks. Chem. Soc. Rev. 41, 6010–6022 (2012).

    Article  CAS  PubMed  Google Scholar 

  203. Patel, H. A. et al. High capacity carbon dioxide adsorption by inexpensive covalent organic polymers. J. Mater. Chem. 22, 8431–8437 (2012).

    Article  CAS  Google Scholar 

  204. Lin, R.-B. & Chen, B. Hydrogen-bonded organic frameworks: chemistry and functions. Chem 8, 2114–2135 (2022).

    Article  CAS  Google Scholar 

  205. Li, P., Ryder, M. R. & Stoddart, J. F. Hydrogen-bonded organic frameworks: a rising class of porous molecular materials. Acc. Mater. Res. 1, 77–87 (2020).

    Article  CAS  Google Scholar 

  206. Brinker, C. J. Porous inorganic materials. Curr. Opin. Solid State Mater. Sci. 1, 798–805 (1996).

    Article  ADS  CAS  Google Scholar 

  207. Park, M., Leahey, E. & Funk, R. J. Papers and patents are becoming less disruptive over time. Nature 613, 138–144 (2023).

    Article  ADS  CAS  PubMed  Google Scholar 

  208. Borsley, S., Gallagher, J. M., Leigh, D. A. & Roberts, B. M. W. Ratcheting synthesis. Nat. Rev. Chem. 8, 8–29 (2024).

    Article  PubMed  Google Scholar 

  209. Astumian, R. D. Kinetic Asymmetry and directionality of nonequilibrium molecular systems. Angew. Chem. Int. Ed. 63, e202306569 (2024).

    Google Scholar 

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Acknowledgements

Financial support from Northwestern University and the Starry Night Science Fund of Zhejiang University Shanghai Institute for Advanced Study (Grant No. SN-ZJU-SIAS-006) is gratefully acknowledged.

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Author notes

  1. These authors contributed equally: Long Zhang, Huang Wu, Xuesong Li.

Authors and Affiliations

  1. Department of Chemistry, Northwestern University, Evanston, IL, USA

    Long Zhang, Huang Wu, Xuesong Li & J. Fraser Stoddart

  2. Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China

    Huang Wu & J. Fraser Stoddart

  3. Department of Chemistry, University of Wyoming, Laramie, WY, USA

    Xuesong Li

  4. Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou, China

    Hongliang Chen & J. Fraser Stoddart

  5. ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China

    Hongliang Chen & J. Fraser Stoddart

  6. Department of Physics and Astronomy, University of Maine, Orono, ME, USA

    R. Dean Astumian

  7. School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia

    J. Fraser Stoddart

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  1. Long Zhang
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L.Z., H.W. and X.L. contributed equally to this manuscript. All authors contributed to every aspect of the manuscript.

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Glossary

Brownian motion

The random motion of particles suspended in a liquid or a gas resulting from their collisions with other particles.

Catenane

A molecule containing two or more topologically linked macrocyclic component parts.

Clipping

A synthetic protocol involving the macrocyclization of a ring around a template (for example, a ring or dumbbell) to form a mechanical bond.

Co-conformation

The spatial arrangement of the component parts affording distinction between mechanostereoisomers, which can be interconverted by translation, pirouetting or rocking motions constrained by the mechanical bond.

Daisy chain

A rotaxane comprising a number n of covalently bridged ring–axle component parts, the mechanical bonds of which give rise to cyclic ([cn]daisy chains) or acyclic ([an]daisy chains) oligomeric or polymeric architectures.

Dumbbell

A component part of a rotaxane consisting of an axle and stoppers.

Energy ratchet

A molecular machine that achieves directed transport-biased Brownian motion by a ratcheting mechanism that involves the raising and lowering of both kinetic barriers and thermodynamic wells.

Information ratchet

A molecular machine that achieves directed transport-biased Brownian motion by a ratcheting mechanism that involves raising and lowering kinetic barriers, depending on the state of the system, such as whether a binding site is occupied.

Kinetic asymmetry

Situation in which the rate constants of reactions leading from an intermediate state to several different product states are very different from each other. This factor is the key one in determining whether a molecular machine can use energy-driven fluctuations or catalysis to perform work on the environment.

Mechanical bond

An entanglement in space between two or more molecular entities (component parts) such that they cannot be separated without breaking or distorting chemical bonds between atoms.

Mechanically interlocked molecules

Molecules containing mechanical or topological entanglements.

Microscopic reversibility

A principle according to which the ratio of probabilities of a trajectory and its microscopic reverse is equal to the exponential of the energy exchanged with the environment.

Molecular motor

A type of molecular machine that converts energy from an external source into unidirectional movement on a molecular scale, including linear molecular motor and rotary molecular motor.

Molecular pump

A molecular machine that can use energy from light, chemical catalysis or external modulation of thermodynamic parameters to drive the formation and maintenance of a chemical potential difference between two or more molecular species.

Non-equilibrium pumping equality

Exact expression for the non-equilibrium steady state concentration ratio between two states that is the product of the equilibrium constant and a directionality, also known as a ratcheting constant.

Non-equilibrium steady state

A state in which a system has been forced away from a thermodynamically stable state but in which the concentration of the different molecular species does not change with time. A non-equilibrium steady state is characterized by a continual steady energy dissipation.

Pseudorotaxane

A complex resembling a rotaxane without stoppers, leaving the ring(s) free to dissociate from the axle — its component parts are held together chiefly by noncovalent bonds rather than by mechanical bonds.

Pseudo-dumbbell

A situation in which at least one or more rings exist in equilibrium with a dumbbell because either one or both of its stoppers are absent. When only one of the two stoppers is absent, the pseudo-dumbbell is sometimes referred to as a half-dumbbell.

Pumping cassette

A structure in which a binding (recognition) site is surrounded by switchable barriers (molecular speed bumps).

Ratchet mechanism

A characteristic of the operating mechanism of many biological molecular machines that serves to limit either rotary or linear motion to occur in only one direction. A Brownian ratchet uses input energy to prevent backward motion rather than to cause forward motion.

Rotaxane

A molecule comprising at least one macrocyclic ring component, with at least one linear component threaded through the ring(s) and terminated by bulky end-groups (stoppers) large enough to prevent dethreading.

Stopper

A bulky group in the dumbbell of a rotaxane that prevents the ring from slipping off the dumbbell.

Trajectory thermodynamics

Focuses on forward and microscopic reverse trajectories between the states, as well as on the relations between the probabilities of these trajectories and the energy exchanged with the environment dictated by the principle of microscopic reversibility.

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Zhang, L., Wu, H., Li, X. et al. Artificial molecular pumps. Nat Rev Methods Primers 4, 13 (2024). https://doi.org/10.1038/s43586-024-00291-w

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