H-Bonding Supramolecular Assemblies of PTCDI Molecules on the Au(111) Surface

Abstract

Using a combination of scanning tunneling microscopy (STM) in ultrahigh vacuum (UHV) and a systematic theoretical method based on considering all possible hydrogen bond connections between molecules with subsequent density functional theory (DFT) calculations, we studied supramolecular assemblies of highly symmetrical rectangular PTCDI molecules on the Au(111) surface. We show, using a systematic prediction procedure followed by ab initio density functional calculations, that just over 10 monolayer structures are possible assuming two molecules in the primitive cell, some of which would appear indistinguishable in the STM images. By breaking down these structures into distinct assemblies, we predict six possible phases. Two of these had been observed previously: a canted phase seen on a number of surfaces including Au(111) and a brick wall phase seen so far only on the NaCl(001) surface. Using STM imaging of PTCDI molecules on the Au(111) surface in ultrahigh vacuum, we discovered a completely new “domino” phase, also predicted by our theory, in which molecules attach to each other rather like dominoes, to form squares repeated periodically across the surface. The interaction of the molecules with the gold surface seems to influence the orientation of the phases but not necessarily their stability.

Experimental and theoretical analysis of H-bonded supramolecular assemblies of PTCDA molecules

“…In order to consider all possible structures these molecules can form, we use a systematic approach developed earlier for adenine, 56 melamine, 57 and PTCDI. 58 This previous work also demonstrated how the symmetry of molecules may affect the number of monolayers they are able to form: we show that the number of possible structures these rather symmetric molecules can form with each other is significantly limited.…”

“…All our calculations are for a twodimensional gas and neglect explicitly their interaction with the substrate. In order to construct all possible structures, a systematic approach described in the previous work [56][57][58] was used consisting of the following steps: ͑i͒ identification of all peripheral binding sites the molecule has that can participate in a hydrogen bonding with another molecule; ͑ii͒ construct all possible dimers; ͑iii͒ by connecting molecules, using dimer rules, all possible unit cells are constructed having a predefined number of molecules; ͑iv͒ all possible chains ͑i.e., one-dimensional structures͒ are built for every unit cell; ͑v͒ by attaching chains parallel to each other, all possible 2D periodic structures are formed; ͑vi͒ stabilities of the predicted in this way assemblies are estimated by summing up all dimer energies ͑per cell͒ and, ͑vii͒ the most stable predicted structures are then fully relaxed using an ab initio method to finally obtain their geometries and binding energies.…”

Two-Dimensional 1,3,5-Tris(4-carboxyphenyl)benzene Self-Assembly at the 1-Phenyloctane/Graphite Interface Revisited

“…10 Single 11,12 and multicomponent 1,[13][14][15][16] self-assembled porous nanoarchitectures can be achieved through hydrogen bonding. Building blocks based on molecule having carboxyl groups (COOH) are especially interesting because these groups can form 2 H-Bonds (O-H· · · O).…”

Localized intermolecular electronic coupling in two-dimensional self-assembled 3,4,9,10-perylenetetracarboxylic diimide nanoarchitectures

“…1d shows the PTCDI network on Au(111) aer 2 h postannealing at 50 C. Molecules are now forming a new twodimensional nanoarchitecture that has not been predicted by previous calculations. 15 The model of this structure is presented in Fig. 1e Fig.…”