Selectively Scissoring Hydrogen-Bonded Cytosine Dimer Structures Catalyzed by Water Molecules

A single-molecule-level understanding of the activity of solvating water molecules in hydrogen-bonded assemblies would provide insights into the properties of the first hydration shells. Herein, we investigate the solvation of one of the DNA bases, cytosine, whose glassy-state network formed on Au(111) contains diverse types of hydrogen-bonded dimer configurations with hierarchical strengths. Upon water exposure, a global structural transformation from interwoven chain segments to extended chains was identified by scanning tunneling microscopy and atomic force microscopy. Density functional theory calculation and coarse-grained molecular dynamics simulation indicate that water molecules selectively break the weak-hydrogen-bonded dimers at T-junctions, while the stable ones within chains remain intact. The resulting hydrated chain segments further self-assemble into molecular chains by forming strong hydrogen bonds and spontaneously releasing water molecules. Such an intriguing transformation cannot be realized by thermal annealing, indicating the dynamic nature of water molecules in the regulation of hydrogen bonds in a catalytic manner.