PAPER: Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch

Ning Y, Cramer JR, Nuermaimaiti A, Svane K, Yu M, Lægsgaard E, Besenbacher F, Xue QK, Ma X, Hammer B, Gothelf KV, Linderoth TR

J Chem Phys. 2015 Mar 14, 142 (10), 101922. doi:10.1063/1.4908062.

  • Interdisciplinary Nanoscience Center (iNANO) and Danish National Research Foundation: Danish-Chinese Centre for Self-Assembly and Function of Molecular Nanostructures on Surfaces, 8000 Aarhus C, Denmark.
  • Institute of Physics, The Chinese Academy of Sciences, Beijing 100190, China


Supra-molecular self-assembly on surfaces often involves molecular conformational flexibility which may act to enrich the variation and complexity of the structures formed. However, systematic and explicit investigations of how molecular conformational states are selected in surface self-assembly processes are relatively scarce. Here, we use a combination of high-resolution scanning tunneling microscopy and Density Functional Theory (DFT) calculations to investigate self-assembly for a custom-designed molecule capable of assuming eight distinct surface conformations (four enantiomeric pairs). The conformations result from binary positions of n = 3 naphtalene units on a linear oligo(naphthylene-ethynylene) backbone. On Au(111), inter-molecular interactions involving carboxyl and bulky tert-butyl-phenyl functional groups induce the molecules to form two ordered phases with brick-wall and lamella structure, respectively. These structures each involve molecules in two conformational states, and there is a clear separation between the conformers involved in the two types of structures. On Cu(111), individual molecules isolated by carboxylate-substrate binding show a distribution involving all possible conformational states. Together these observations imply selection and adaptation of conformational states upon molecular self-assembly. From DFT modeling and statistical analysis of the molecular conformations, the observed selection of conformational states is attributed to steric interaction between the naphthalene units. The present study enhances our understanding of how ordering and selection of molecular conformations is controlled by intermolecular interactions in a complex situation with many distinct conformational states for the participating molecules.

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