IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-61364-2.html
   My bibliography  Save this article

Controlled assembly of rotaxane translational isomers using dual molecular pumps

Author

Listed:
  • Christopher K. Lee

    (University of New South Wales)

  • Jake P. Violi

    (University of New South Wales)

  • William A. Donald

    (University of New South Wales)

  • J. Fraser Stoddart

    (University of New South Wales
    The University of Hong Kong
    Northwestern University
    Northwestern University)

  • Dong Jun Kim

    (University of New South Wales)

Abstract

The ability to control the relative motion between different components of molecules with precision is a cornerstone of synthetic nanotechnology. Mechanically interlocked molecules such as rotaxanes offer a platform for exploring this control by means of the positional manipulation of their components. Here, we demonstrate the use of a molecular dual pump to achieve the assembly of translational isomers with high efficiency and accuracy. By harnessing pumping cycles, rings can be guided selectively along a molecular axle, resulting in two sets of distinct translational isomers of [2]- and [3]rotaxanes. These isomers, produced in high yields, are characterized by mass spectrometry in addition to one- and two-dimensional nuclear magnetic resonance spectroscopy, which collectively reveal the location of the rings in the rotaxanes. Nuclear Overhauser effect spectroscopy confirms the spatial localization of rings, while diffusion ordered spectroscopy measurements quantifies the differences in hydrodynamic properties between the rotaxanes. This research supports the status of molecular pumps as a robust tool for precise nanoscale assembly, while advancing the practice of molecular machinery at the frontiers of synthetic nanotechnology.

Suggested Citation

  • Christopher K. Lee & Jake P. Violi & William A. Donald & J. Fraser Stoddart & Dong Jun Kim, 2025. "Controlled assembly of rotaxane translational isomers using dual molecular pumps," Nature Communications, Nature, vol. 16(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61364-2
    DOI: 10.1038/s41467-025-61364-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-61364-2
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-61364-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. David A. Leigh & Jenny K. Y. Wong & François Dehez & Francesco Zerbetto, 2003. "Unidirectional rotation in a mechanically interlocked molecular rotor," Nature, Nature, vol. 424(6945), pages 174-179, July.
    2. Eugene Klyshko & Justin Sung-Ho Kim & Lauren McGough & Victoria Valeeva & Ethan Lee & Rama Ranganathan & Sarah Rauscher, 2024. "Functional protein dynamics in a crystal," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Elan Z. Eisenmesser & Oscar Millet & Wladimir Labeikovsky & Dmitry M. Korzhnev & Magnus Wolf-Watz & Daryl A. Bosco & Jack J. Skalicky & Lewis E. Kay & Dorothee Kern, 2005. "Intrinsic dynamics of an enzyme underlies catalysis," Nature, Nature, vol. 438(7064), pages 117-121, November.
    4. Yansong Ren & Romain Jamagne & Daniel J. Tetlow & David A. Leigh, 2022. "A tape-reading molecular ratchet," Nature, Nature, vol. 612(7938), pages 78-82, December.
    5. James S. Fraser & Michael W. Clarkson & Sheena C. Degnan & Renske Erion & Dorothee Kern & Tom Alber, 2009. "Hidden alternative structures of proline isomerase essential for catalysis," Nature, Nature, vol. 462(7273), pages 669-673, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. repec:plo:pone00:0015827 is not listed on IDEAS
    2. repec:plo:pone00:0040897 is not listed on IDEAS
    3. Tomoki Nakajima & Shohei Tashiro & Masahiro Ehara & Mitsuhiko Shionoya, 2023. "Selective synthesis of tightly- and loosely-twisted metallomacrocycle isomers towards precise control of helicity inversion motion," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    4. Eike C. Schulz & Andreas Prester & David Stetten & Gargi Gore & Caitlin E. Hatton & Kim Bartels & Jan-Philipp Leimkohl & Hendrik Schikora & Helen M. Ginn & Friedjof Tellkamp & Pedram Mehrabi, 2025. "Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    5. Timothy R Lezon & Ivet Bahar, 2010. "Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology," PLOS Computational Biology, Public Library of Science, vol. 6(6), pages 1-12, June.
    6. Emma L. Hollis & Michael N. Chronias & Carlijn L. F. Beek & Paul J. Gates & Beatrice S. L. Collins, 2025. "[1,n]-Metal migrations for directional translational motion at the molecular level," Nature Communications, Nature, vol. 16(1), pages 1-8, December.
    7. Seonggon Lee & Hosung Ki & Donghwan Im & Jungmin Kim & Yunbeom Lee & Jain Gu & Alekos Segalina & Jun Heo & Yongjun Cha & Kyung Won Lee & Doyeong Kim & Jeongho Kim & Rory Ma & Jae Hyuk Lee & Hyotcherl , 2025. "Ultrafast structural dynamics of carbon–carbon single-bond rotation in transient radical species at non-equilibrium," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    8. Santiago Esteban-Martín & Robert Bryn Fenwick & Jörgen Ådén & Benjamin Cossins & Carlos W Bertoncini & Victor Guallar & Magnus Wolf-Watz & Xavier Salvatella, 2014. "Correlated Inter-Domain Motions in Adenylate Kinase," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-7, July.
    9. Adriana Coricello & Alanya J. Nardone & Antonio Lupia & Carmen Gratteri & Matthijn Vos & Vincent Chaptal & Stefano Alcaro & Wen Zhu & Yuichiro Takagi & Nigel G. J. Richards, 2024. "3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Gregory D Friedland & Nils-Alexander Lakomek & Christian Griesinger & Jens Meiler & Tanja Kortemme, 2009. "A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family," PLOS Computational Biology, Public Library of Science, vol. 5(5), pages 1-16, May.
    11. repec:plo:pone00:0029377 is not listed on IDEAS
    12. Antony D. St-Jacques & Joshua M. Rodriguez & Matthew G. Eason & Scott M. Foster & Safwat T. Khan & Adam M. Damry & Natalie K. Goto & Michael C. Thompson & Roberto A. Chica, 2023. "Computational remodeling of an enzyme conformational landscape for altered substrate selectivity," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    13. Jiaqi Liang & Shuai Lu & Yang Yang & Yun-Jia Shen & Jin-Ku Bai & Xin Sun & Xu-Lang Chen & Jie Cui & Ai-Jiao Guan & Jun-Feng Xiang & Xiaopeng Li & Heng Wang & Yu-Dong Yang & Han-Yuan Gong, 2023. "Thermally-induced atropisomerism promotes metal-organic cage construction," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    14. Giacomo Janson & Gilberto Valdes-Garcia & Lim Heo & Michael Feig, 2023. "Direct generation of protein conformational ensembles via machine learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    15. Maciej Majewski & Adrià Pérez & Philipp Thölke & Stefan Doerr & Nicholas E. Charron & Toni Giorgino & Brooke E. Husic & Cecilia Clementi & Frank Noé & Gianni Fabritiis, 2023. "Machine learning coarse-grained potentials of protein thermodynamics," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    16. Torgeir R Hvidsten & Astrid Lægreid & Andriy Kryshtafovych & Gunnar Andersson & Krzysztof Fidelis & Jan Komorowski, 2009. "A Comprehensive Analysis of the Structure-Function Relationship in Proteins Based on Local Structure Similarity," PLOS ONE, Public Library of Science, vol. 4(7), pages 1-9, July.
    17. repec:plo:pcbi00:1002000 is not listed on IDEAS
    18. Diego F. Gauto & Pavel Macek & Duccio Malinverni & Hugo Fraga & Matteo Paloni & Iva Sučec & Audrey Hessel & Juan Pablo Bustamante & Alessandro Barducci & Paul Schanda, 2022. "Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    19. Dong Long & Rafael Brüschweiler, 2011. "In Silico Elucidation of the Recognition Dynamics of Ubiquitin," PLOS Computational Biology, Public Library of Science, vol. 7(4), pages 1-9, April.
    20. Bakalis, Evangelos, 2012. "Explicit propagators for a random walker and unidirectionality on linear chains," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(11), pages 3093-3101.
    21. Tiberiu Teşileanu & Lucy J Colwell & Stanislas Leibler, 2015. "Protein Sectors: Statistical Coupling Analysis versus Conservation," PLOS Computational Biology, Public Library of Science, vol. 11(2), pages 1-20, February.
    22. Fabian Paul & Thomas R Weikl, 2016. "How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates," PLOS Computational Biology, Public Library of Science, vol. 12(9), pages 1-17, September.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61364-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.