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H-Bond Self-Assembly: Folding versus Duplex Formation.

Diego Núñez-Villanueva1, Giulia Iadevaia1, Alexander E Stross1

  • 1Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K.

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Oligomers with H-bonding sites form duplexes or fold. Rigid backbones favor duplexes, enabling synthetic information molecules, while flexible backbones lead to folding and weaker duplexes.

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Area of Science:

  • Supramolecular chemistry
  • Chemical biology
  • Organic chemistry

Background:

  • Linear oligomers with hydrogen-bonding donor (D) and acceptor (A) sites can form duplexes or fold.
  • Competing equilibria between intermolecular duplex formation and intramolecular folding influence molecular assembly.

Purpose of the Study:

  • To quantify the competing equilibria of duplex formation and folding in various oligomer systems.
  • To investigate the impact of backbone flexibility and recognition site design on self-assembly.

Main Methods:

  • NMR titration and dilution experiments were employed to study seven different oligomer architectures.
  • Analysis focused on quantifying self-association constants and identifying dominant folding or duplex formation pathways.

Main Results:

  • Homo-sequence dimers (AA·DD) consistently formed duplexes without competing folding.
  • Hetero-sequence dimers (AD) showed duplex formation, but stability was reduced by monomer folding in flexible-backbone systems.
  • Flexible backbones (≥5 rotatable bonds) favored intramolecular H-bonding, decreasing duplex stability by 1-2 orders of magnitude.
  • Rigid backbones (<5 rotatable bonds) prevented intramolecular interactions, allowing for stable duplex formation.

Conclusions:

  • Backbone rigidity is crucial for preventing competing folding equilibria and enabling stable intermolecular interactions.
  • Oligomers with rigid backbones are promising for developing longer, sequence-selective synthetic information molecules.
  • Understanding these competing equilibria is key for designing functional supramolecular systems.