Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional (2D) materials is a developing field driven by the interest in functionalization of 2D materials in order to tune their electronic properties. This has resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy (STM). The review covers three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moiré pattern present on 2D materials grown on substrates. We also see that modification of intermolecular interactions and molecule-substrate interactions influences the assembly drastically and that 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moiré pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled, acceptor and donor type, organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from atomically thin crystals, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging from flexible electronics and OLEDs to novel electronic devices and spintronics. * This is slightly expanded version of the review published in Nanotechnology 28(2017), 082001

Two-dimensional (2D) metal–organic frameworks (MOFs) have been recently proposed as a flexible material platform for realizing exotic quantum phases including topological and anomalous quantum Hall insulators. Experimentally, direct synthesis of 2D MOFs has been essentially confined to metal substrates, where the strong interaction with the substrate masks the intrinsic electronic properties of the MOF. In addition to electronic decoupling from the underlying metal support, synthesis on weakly interacting substrates (e.g., graphene) would enable direct realization of heterostructures of 2D MOFs with inorganic 2D materials. Here, we demonstrate synthesis of 2D honeycomb MOFs on epitaxial graphene substrate. Using low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM) complemented by density-functional theory (DFT) calculations, we show the formation of a 2D band structure in the MOF decoupled from the substrate. These results open the experimental path toward MOF-based designer electronic materials with complex, engineered electronic structures.

π-conjugated organic molecules tend to adsorb in a planar configuration on graphene irrespective of their charge state. In contrast, here we demonstrate charging-induced strong structural relaxation of tetrafluorotetracyanoquinodimethane (FTCNQ) on epitaxial graphene on Ir(111) (G/Ir(111)). The work function modulation over the graphene moiré unit cell causes site-selective charging of FTCNQ. Upon charging, the molecule anchors to the face-centered cubic sites of the G/Ir(111) moiré through one or two cyano groups. The reaction is reversible and can be triggered on a single molecule by moving it between different adsorption sites. We introduce a model taking into account the trade-off between tilt-induced charging and reduced van der Waals interactions, which provides a general framework for understanding charging-induced structural relaxation on weakly interacting substrates. In addition, we argue that the partial sp rehybridization of the underlying graphene and the possible bonding mechanism between the cyano groups and the graphene substrate are also relevant for the complete understanding of the experiments. These results provide insight into molecular charging on graphene, and they are directly relevant for potential device applications where the use of molecules has been suggested for doping and band structure engineering.

We report on molecular self-assembly employing a host−guest architecture to pattern the growth of molecules on graphene model surface. Under suitable conditions, the 1,3,5-benzenetribenzoic acid (BTB) selfassembles into an extended honeycomb mesh on graphene on Ir(111), with the molecules in the network being stabilized by linear hydrogen bonds between the carboxylic groups. The nanopores of the mesh are used to host and govern the assembly of cobalt phthalocyanine (CoPC) guest molecules. We characterize the assembled structures structurally and electronically using low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. At a coverage higher than one CoPc per pore, the flexible hydrogen bonds of the host network undergo stretching to accommodate two CoPCs in a single pore. When the pores are uniformly doubly occupied, the guest molecules arrange into a herringbone pattern. This minimizes the energy cost associated with the stretching and twisting of the hydrogen bonds between the BTB molecules. The phenomenon observed here can be used to tailor molecular assemblies on graphene to controllably modify its properties. In addition, it allows the formation of guest monomers and dimers stabilized mechanically on the surface of graphene, an archetypical weakly interacting substrate.

The energetics and dynamics of the various phases of decanethiolate self-assembled monolayers on Au(111) surfaces were studied with scanning tunneling microscopy. We have observed five different phases of the decanethiolate monolayer on Au(111): four ordered phases (β, δ, χ*, and φ) and one disordered phase (ε). We have determined the boundary free energies between the disordered and order phases by analyzing the thermally induced meandering of the domain boundaries. On the basis of these results, we are able to accurately predict the two-dimensional phase diagram of the decanethiolate/Au(111) system. The order-disorder phase transition of the χ* phase occurs at 295 K, followed by the order-disorder phase transition of the β phase at 325 K. Above temperatures of 325 K, only the densely packed φ and disordered ε phases remain. Our findings are in good agreement with the phase diagram of the decanethiolate/Au(111) system that was put forward by Poirier et al. [Langmuir 2001, 17 (4), 1176-1183].