Studies of the structure and phase transitions of nano-confined pentanedithiol and its application in directing hierarchical molecular assemblies on Au(1 1 1)

Abstract

Directing molecular devices into pre-designed integrated electronic circuits while enforcing selectivity and hierarchy is an inherent challenge for molecular electronics. Here we explore ways to direct the assembly of electrically-active molecular monolayers into specific locations as well as controlling their internal organization. We have accomplished this by two consecutive surface reactions: (1) forming pentanedithiol (C5DT) domains within an inert alkanethiol self-assembled monolayer (SAM) on Au; and (2) selectively binding porphyrin derivatives to the C5DT domains. The C5DT domains were fabricated by phase segregation during co-adsorption from a mixed C5DT/dodecanethiol (C12) solution and nanografting with Atomic Force Microscopy (AFM). AFM revealed that co-absorbed and nanografted C5DT domains were in a standing-up phase and scanning tunneling microscopy (STM) showed that their molecular organization within about 5 nm, 40 nm, 50 nm and 120 nm domains, was dependent upon the size of the domain, such that structure of the C5DT transitions from ( × ) R30°, to (2 × 2), and ultimately to a disordered phase with increasing domain size. This is due to the varying degrees of influence of the surrounding C12; providing sufficient van der Waals interactions as well as a geometric confinement to stabilize the standing-up phase of the C5DT. Understanding the molecular configuration of dithiol SAMs affords their use as a reactive template to subsequently bind active head groups. As a proof of principle, porphyrins with a pendant pentafluorophenyl ring were attached to the C5DT domains by a ‘click’ reaction between the fluorinated ring and the free thiol on the surface. From AFM and STM, these porphyrin derivatives reacted selectively with the C5DT domains with some porphyrins binding directly to the C5DT, subsequently allowing additional localized porphyrin deposition through pi-stacking.