Two-dimensional self-assembled structures of adenine molecules: Modeling and simulation

Keiko Shinoda, Wataru Shinoda, Chee Chin Liew, Seiji Tsuzuki, Yoshitada Morikawa, Masuhiro Mikami

Research output: Contribution to journalArticlepeer-review

22 Citations (Scopus)


Self-assembly of adenine molecules deposited on a Cu(1 1 1) surface shows some characteristic hydrogen-bonding network patterns, such as hexagonal and 'double-chain'. In order to understand the emergence of energetically less favorable 'double-chain' structure, in which adenine molecules form two rows, possible molecular arrangements in the 'double-chain' structure are investigated by potential energy surface (PES) calculations between two single chains. A series of PES calculations elucidates that there are various stable molecular arrangements for the chain pair models: some of the models have both hexagonal and 'double-chain' (I-type) hydrogen-bonding patterns, while the others have only the latter pattern (II-type). Molecular dynamics simulations starting from the obtained 'double-chain' structures are also performed to assess the thermal stability of the structure. It is revealed that some of the II-type 'double-chain' structures remain even at 300 K, while all I-type ones transform into hexagonal arrays. The former result reminds us that the II-type 'double-chain' structures should be observed at room temperature in the STM experiment.

Original languageEnglish
Pages (from-to)109-120
Number of pages12
JournalSurface Science
Issue number2-3
Publication statusPublished - May 10 2004
Externally publishedYes


  • Biological molecules - nucleic acids
  • Copper
  • Molecular dynamics
  • Self-assembly
  • Surface electronic phenomena (work function, surface potential, surface states, etc.)
  • Surface energy

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Surfaces and Interfaces
  • Surfaces, Coatings and Films
  • Materials Chemistry


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