Coarse-Grained Modeling of On-Surface Self-Assembly of Mixtures Comprising Di-Substituted Polyphenyl-Like Compounds and Metal Atoms of Different Sizes

Abstract

We use coarse-grained molecular dynamics simulations to investigate the phase behavior of binary mixtures of disubstituted polyphenyl-like compounds and metal atoms of different sizes. We have estimated the possible on-surface behavior that could be useful for the target design of particular ordered networks. We have found that due to the variation of system conditions, we can observe the formation of the parallel, square, and triangular networks, Archimedean tessellation, and "spaghetti wires." All of these structures have been characterized by various order parameters.

Off-Lattice Coarse-Grained Model of Surface-Confined Metal–Organic Architectures

“…When constructing the model, it was assumed that sizes of the functional group and the coordinating metal center were the same. On the one hand, the effect of metal atom size was recently studied by Baran . On the other hand, the covalent diameters of copper (2.64 Å), iron (2.64 Å), and cobalt (2.52 Å) are indeed close to the size of functional groups considered in these work (Figure ).…”

“…A detailed theoretical or computer simulation study of complex SMONs on the atomistic level can also be arduous. Application of coarse-grained models is one possible solution to this problem. ,,,− Depending on how the translational and rotational degrees of freedom of the adsorbed molecules and atoms are considered, such models can be discrete (lattice) or continuous (off-lattice). The adsorbate–adsorbate interactions are usually assumed to be short-ranged.…”

“…46−61 Continuous models of SMONs are much less common. In a recent work, 27 Baran had studied how the metal/ligand ratio and size of the coordinating metal center affect the self-assembly of SMONs containing linear linker molecules. The observed maximum coordination number was shown to depend on the size of the metal center.…”

On-surface Ullmann coupling of halo-derivatives of arenes: Monte Carlo simulations for tetracene

“…This refers especially to the number and intramolecular distribution of halogen substituents in PAHs monomers, aiming at the synthesis of the polymer with predefined architecture. To facilitate the optimization of the monomeric units, computer-aided methods like quantum mechanical (QM) modelling, molecular dynamics (MD), and Monte Carlo (MC) simulations have often been applied [35][36][37][38][39][40][41][42][43][44][45]. While QM calculations have been used mainly to determine energetics and mechanisms of intermolecular bonding [35][36][37][38], the other methods have been much less widespread, and they have drawn considerable attention quite recently, in spite of better scaling properties and being relatively less complicated [39][40][41][42][43][44][45][46].…”

“…To facilitate the optimization of the monomeric units, computer-aided methods like quantum mechanical (QM) modelling, molecular dynamics (MD), and Monte Carlo (MC) simulations have often been applied [35][36][37][38][39][40][41][42][43][44][45]. While QM calculations have been used mainly to determine energetics and mechanisms of intermolecular bonding [35][36][37][38], the other methods have been much less widespread, and they have drawn considerable attention quite recently, in spite of better scaling properties and being relatively less complicated [39][40][41][42][43][44][45][46]. Among diverse computational chemistry tools, the coarse-grained MC simulations turned out to be an effective way of predicting the architecture of metal-organic intermediates, as confirmed by the corresponding experimental data -obtained, for example, with STM imaging of adsorbed overlayers [11][12][13][14].…”