Mechanism of two-dimensional superstructure formation of self-assembled adenine molecules

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

Trans. MRS-J 29 3755-3758 (2004).

One of the DNA bases, adenine molecules spontaneously form superstructures on the Cu(111) surface. Under an experimental condition, a characteristic chain structure, in which adenine molecules form two rows, i.e. 'double-chain', was observed, coexisting with a hexagonal structure, though the former is less favorable than the latter in energy. In this study, molecular arrangements of the 'double-chain' structure were analyzed. A series of inter-chain potential energy surface (PES) calculations revealed that there were two types of two-chain systems: one had both hexagonal and double-chain structures, and the other had only double-chain structures, as the stable structures. Furthermore, thermal stability of the double-chain structures was investigated by means of two-dimensional molecular dynamics (MD) simulation. The MD simulation revealed that some double-chain structures were stable even at 300 K and some transformed into a hexagonal structure. The former accounts for the coexistence of double-chain and hexagonal structures observed in the STM experiment, and the latter suggests that an energetically favorable hexagonal structure can be attained by way of a double-chain structure.