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

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-chainʹ. In order to understand the emergence of energetically less favorable `double-chainʹ structure, in which adenine molecules form two rows, possible molecular arrangements in the `double-chainʹ 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-chainʹ (I-type) hydrogen-bonding patterns, while the others have only the latter pattern (II-type). Molecular dynamics simulations starting from the obtained `double-chainʹ structures are also performed to assess the thermal stability of the structure. It is revealed that some of the II-type `double-chainʹ 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-chainʹ structures should be observed at room temperature in the STM experiment.