Influence of Deoxyribose Group on Self-Assembly of Thymidine on Au(111)

Abstract

Using scanning tunneling microscopy (STM), we investigate the self-assembled structures and current-induced phase transition of one nucleoside species, thymidine (TD) on Au(111). By comparing the previous work on DNA nucleic acid base thymine on the same surface, we find that the deoxyribose groups of TD molecules remarkably enhance the intermolecular interaction and drive the formation of a dimer structure even at low temperature. At room temperature, TD molecules aggregate into well-ordered dimer islands. A two-dimensional (2D) gas-like phase of mobile TD molecules is also found surrounding the islands, and it can be transformed into the dimer structure. Furthermore, a new phase, a parallel-line structure, was observed gradually developing around the dimer domains under consecutive scanning. These molecular lines can be produced from both the gas-like phase and the dimer. First-principle calculations illustrate the optimized molecular superstructures in both phases.