Self-assembled monolayers (SAMs) of terphenylthiol (TP0) prepared on Au(111) from ethanolic solution at room temperature and subsequently annealed at different temperatures of up to 473 K were investigated using scanning tunneling microscopy and infrared reflection absorption spectroscopy. Upon annealing, the TP0 adlayer formed a series of different structural phases with different molecular arrangements. Our results show that SAMs prepared at RT without annealing and SAMs annealed at 313 K exhibited the formation of a closely packed “α” structure where TP0 molecular axes are orientated almost upright. The formation of the α-phase was accompanied by the formation of a loosely packed phase (β-phase). During annealing from 333 to 473 K, the results revealed the formation of different structural phases, namely, γ, δ, ε, σ, and ϕ. With the exception of the ϕ-phase, the phases were found to form loosely packed structures with the molecular axes largely tilted away from surface normal but do not form “flat-lying” phases. Surprisingly, upon annealing at 453 K, the SAMs exhibited a phase transition to a higher dense network of molecular structure (ϕ-phase) with almost upright standing molecules. An additional annealing at 463 K led to a significant increase in the size of the well-ordered domains of the ϕ-phase at the expense of their density. At the same time, a partial desorption of the TP0-SAMs was noticed to take place. The formation of a densely packed phase upon annealing and subsequently desorption of TP0 molecules from this state completely contradicts the behavior of n-alkanethiol and other oligophenylthiol SAMs, in which desorption occurs from lying-flat geometry. The ϕ-phase, which was the only one remaining on the surface, did not cover more than 30% of the gold surface area. A further increase of the annealing temperature to 473 K caused a substantial increase in the number of the desorbed molecules. Therefore, a remarkable reduction in both the size and density of the ordered domains of the ϕ-phase was observed. On the other hand, the annealing temperature was found to have a significant influence on both the appearance and the shape of the gold islands. Moreover, it has been found that the gold islands, regardless of their shapes, were always covered by standing-up, densely packed, and ordered phases such as the α- and ϕ-phases.

Self-assembled monolayers (SAMs) formed by adsorption of 1,2dibenzyldiselenide (DPMSe) and 1,2-diphenyldiselenide (DBSe) on Au(111) substrates at room temperature have been characterized using scanning tunnelling microscopy, X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, near-edge X-ray absorption fine structure spectroscopy , and lowenergy electron diffraction. Upon adsorption, the Se−Se bonds in DPMSe and DBSe were cleaved on the gold surface to form phenylmethaneselenolate (PMSe) and benzeneselenolate (BSe) species, respectively. Although both PMSe and BSe molecular entities only differ in their structure (an additional methyl group in PMSe), the resulting monolayer films revealed noteworthy dissimilarities regarding their adlayer SAM structure and surface morphology. The molecular adlayer structure and orientation of PMSe and BSe species were found to vary significantly with the immersion time (IT). The resulting PMSe films were poorly organized, and the structure was described by a (4√3 × 2) rectangular unit cell for the SAMs prepared with 24 h of IT. Moreover, the PMSe-SAMs were found to be unstable upon exposure to air for a long time. Our results showed that exposure to air for 48 h results in the formation of small bright ad-islands, which have a height corresponding to that of a single atomic step on the Au(111). Contrary, BSe-SAMs exhibited densely packed and well-ordered monolayers, and two different structural phases were resolved at short and long ITs. The most densely packed structure was obtained for SAMs prepared with very short ITs (10 min). Upon increasing the IT, the SAMs exhibited structural changes to a lower density of molecular packing structure. The spectroscopic data also confirmed this structural transformation by suggesting an upright orientation for BSe-SAMs prepared after short ITs and strongly inclined adsorption geometry for SAMs prepared after long ITs.

The structure and molecular organization of self-assembled monolayers (SAMs) depend on a complex interplay of intermolecular and molecule-substrate interactions, so that even a small change in molecular composition can result in noticeable changes in the SAM structure. Herein we show that decoration of the most basic aromatic SAM constituent, benzenethiol, with two trifluoromethyl groups leads to distinct polymorphism in the respective SAMs, in which the appearance of a specific structural phase or a combination of several different phases is dependent on the parameters of the preparation procedure. High-quality films with a single crystallographic phase and significantly large domains could only be prepared after a short immersion time (5 min) and an additional re-immersion of the sample in pure ethanol at an elevated temperature. A standard 24 h immersion at room temperature led to poorly defined films with a large defect density and only a small portion of the surface covered by well-ordered molecular domains.

By the example of 4-fluorobenzene-1-thiolate (p-FTP) films on Au(111), we show that a long-term postpreparation storage can improve significantly the quality of fluorinated aromatic self-assembled monolayers (SAMs). Whereas the freshly prepared p-FTP films exhibit a polymorphism, with a dominance of a disordered phase, the postpreparation storage triggers a gradual phase transition to a single-phase SAM of exceptional quality. This phase is characterized by the commensurate (16 × √3) structure, a molecular footprint of 23.1 Å 2 , high orientational order, and hardly perceptible borders between individual domains, with sizes exceeding 80 nm. Significantly, the phase transition is accompanied by morphological transformation of the substrate: whereas the freshly prepared films exhibit comparably large Au adatom islands, typical of aromatic SAMs, the long-storage samples rather reveal etch-pits, typical of alkanethiolate SAMs on Au(111), which generally have a high structural order immediately after the preparation. The above results suggest a deep interrelation between the structural order in the SAMs and surface morphology. A further implication is the importance of both thermodynamic and kinetic factors, a delicate interplay of which is presumably responsible for the observed evolution of p-FTP/Au in the present case.