Molecular Level Structural Characterization of Self-Assembled Monolayers of Functionalized Bidentate Aromatic Thiols

Abstract

While molecular-level structural information is readily available for n-alkanethiol self-assembled monolayers (SAMs) on noble metal surfaces, the same cannot be claimed for dithiol-based SAMs due to their lack of long-range-order. This work provides molecular-level structural information on dithiol SAMs by investigating 5-(octyloxy)-1,3-phenylenedimethanethiol (OPDT) SAMs on Au(111) surfaces, using combined high-resolution scanning tunneling microscopy (STM), atomic force microscopy (AFM), and nanolithography. The high coverage OPDT SAMs do not exhibit long-range order. Desorption of these OPDT SAMs leads to the formation of ordered domains known as the striped phases, whose unit mesh is revealed as commensurate with the underlying Au(111) lattice. In these domains, OPDT molecules are lying-down, with the benzene ring and the zigzag plane of the alkyl chain parallel to the Au(111) surface. At the boundaries of these ordered structures, standing-up OPDT molecules are frequently present with an intermolecular space of 1 nm (i.e., 1D ordered structures). Using these ordered structures as internal standards in situ, the structure of the high-coverage OPDT SAMs is revealed: a mixture of standing-up and lying-down molecules randomly distributed on Au(111); as such, these SAMs exhibit little long-range order or ordered domains. The two thiols of each OPDT molecule occupy triple hollow sites on Au(111) surfaces. In the standing-up configuration, the benzene ring is perpendicular to the surface. In the lying-down con-figuration, the benzene ring and zigzag plane of the alkyl chain are parallel to the Au(111) surface. This work represents a high-resolution and molecular-level structural characterization of functionalized dithiol SAMs, furthering our understanding of dithiol molecule−surface interactions and the unique properties of these SAMs.