Effects of inserted methylene groups on structure and flexibility of molecule junction system

The low yield of single-molecule junctions hinders the applications of single-molecule devices. This study investigates the structural flexibilities of a benzenethiol molecule and its methylene-inserted derivatives on a Au(111) surface by density functional theory calculations. The potential energy surface with respect to the tilt of the molecule becomes shallow when an ethylene group (i.e. two methylene units) is inserted at the anchor of the molecule. The deformation of the angle around the thiol group increases the structural energy of noninserted or methylene-inserted molecules. However, as the inserted methylene group rotates freely in the ethylene-inserted molecule, the variation in the structural energy is moderate. Van der Waals interaction does not contribute to the variation in the structural energy for the ethylene-inserted molecule, while the interaction suppresses the increase in the energy for the other cases. These results indicate that inserting an ethylene group at the anchor efficiently improves the yield of junctions.