Chemisorbed and Physisorbed Structures for 1,10-Phenanthroline and Dipyrido[3,2-a:2‘,3‘-c]phenazine on Au(111)

Abstract

Scanning tunneling microscopy (STM) images of 1,10-phenanthroline (PHEN) and dipyrido[3,2-a:2‘,3‘-c]phenazine (DPPZ) on Au(111) are recorded using both in situ and ex situ techniques. The images of PHEN depict regimes of physisorption and chemisorption, whereas DPPZ is only physisorbed. All physisorbed structures are not pitted and fluctuate dynamically, involving aligned (4 × 4) surface domains with short-range (ca. 20 molecules) order for PHEN but unaligned chains with medium-range (ca. 100 molecules) order for DPPZ. In contrast, the chemisorbed PHEN monolayers remain stable for days, are associated with surface pitting, and form a (4 × √13)R46° lattice with long-range order. The density of pitted atoms on large gold terraces is shown to match the density of chemisorbed molecules, suggesting that gold adatoms link PHEN to the surface. For PHEN, chemisorbed and physisorbed adsorbate structures are optimized using plane-wave density-functional theory (DFT) calculations for the surface structure. Realistic binding energies are then obtained adding dispersive corrections determined using complete-active-space self-consistent field calculations using second-order perturbation theory (CASPT2) applied to cluster-interaction models. A fine balance between the large adsorbate−adsorbate dispersive forces, adsorbate−surface dispersive forces, gold ligation energy, and surface mining energy is shown to dictate the observed phenomena, leading to high surface mobility and substrate/surface lattice incommensurability. Increasing the magnitude of the dispersive forces through use of DPPZ, rather than PHEN, to disturb this balance produced physisorbed monolayers without pits and/or surface registration but with much longer-range order. Analogies are drawn with similar but poorly understood processes involved in the binding of thiols to Au(111).

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

“…−175 kcal mol −1 and −115 kcal mol −1 for the L and M polymorphs of C 13 P, respectively (Table 2). This effect is well known for small-molecule interactions in gas-phase dimers and in molecular solids (18)(19)(20)(21)(22)(23)(24), and also for SAMs of small molecules (69,70). However, the magnitude of the effect we see for SAMs of large molecules is unprecedented, not just in absolute value but also in terms of its variations between feasible polymorphs.…”

Conductance of a phenylene-vinylene molecular wire: Contact gap and tilt angle dependence

“…This represents a moderate 1/9 OPV3 monolayer coverage, which guarantees that the molecules in neighboring cells are sufficiently separated ͑i.e., noninteracting͒. [27][28][29][30][31][32][33][34] For the geometry optimizations, as well as for the transport computations, the Brillouin zone integrations were performed on a 3 ϫ 3 k-point Monkhorst-Pack mesh in the plane of the surface. For the calculation of the bulk electronic structure of the gold leads the reciprocal space was sampled on a 3 ϫ 3 ϫ 100 grid, with the denser sampling in the direction of transport.…”

Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

“…This information can be extremely useful, especially if surface pitting is involved. [126] Changing the set-point current changes the average height that the tip scans above the surface, with lower currents moving the tip further away. Taking the tip away from the surface can reduce image quality as the signal to noise ratio decreases and as molecular features become less distinct.…”