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Self-Assembly of Mesoscale Isomers: The Role of Pathways and Degrees of Freedom

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  • Shivendra Pandey
  • Daniel Johnson
  • Ryan Kaplan
  • Joseph Klobusicky
  • Govind Menon
  • David H Gracias

Abstract

The spontaneous self-organization of conformational isomers from identical precursors is of fundamental importance in chemistry. Since the precursors are identical, it is the multi-unit interactions, characteristics of the intermediates, and assembly pathways that determine the final conformation. Here, we use geometric path sampling and a mesoscale experimental model to investigate the self-assembly of a model polyhedral system, an octahedron, that forms two isomers. We compute the set of all possible assembly pathways and analyze the degrees of freedom or rigidity of intermediates. Consequently, by manipulating the degrees of freedom of a precursor, we were able to experimentally enrich the formation of one isomer over the other. Our results suggest a new approach to direct pathways in both natural and synthetic self-assembly using simple geometric criteria. We also compare the process of folding and unfolding in this model with a geometric model for cyclohexane, a well-known molecule with chair and boat conformations.

Suggested Citation

  • Shivendra Pandey & Daniel Johnson & Ryan Kaplan & Joseph Klobusicky & Govind Menon & David H Gracias, 2014. "Self-Assembly of Mesoscale Isomers: The Role of Pathways and Degrees of Freedom," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-7, October.
    • Handle: RePEc:plo:pone00:0108960
    DOI: 10.1371/journal.pone.0108960
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    References listed on IDEAS

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    1. Yu He & Tao Ye & Min Su & Chuan Zhang & Alexander E. Ribbe & Wen Jiang & Chengde Mao, 2008. "Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra," Nature, Nature, vol. 452(7184), pages 198-201, March.
    2. Erik Winfree & Furong Liu & Lisa A. Wenzler & Nadrian C. Seeman, 1998. "Design and self-assembly of two-dimensional DNA crystals," Nature, Nature, vol. 394(6693), pages 539-544, August.
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