Modeling of Ribbon and Oblique Structures of Benzene-1,3,5-triyl-tribenzoic Acid

Abstract

We propose two models describing the self-assembly of intact and deprotonated benzene-1,3,5-triyl-tribenzoic acid (BTB) molecules into the oblique (O) and ribbon (R) phases. The models are also extended to describe the formation of the honeycomb (HON) structure. To determine the intermolecular interaction potentials for the R and O phases, we performed the DFT calculations for the clusters of neutral and charged BTB molecules. The obtained values were used as an input in the Monte Carlo (MC) simulations. The model and MC simulations for the R phase demonstrate how ionic interactions between singly deprotonated BTB molecules lead to the formation of ribbons separated by the interribbon gap, and how these ribbons pack into the ordered two-dimensional structure. The O phase is treated in our model as the structure that might be composed of both intact and singly deprotonated molecules, owing to the occurrence of this phase in polarization switching experiments for positive surface bias. The ground-state analysis and MC modeling for the O and HON structures with the DFT-calculated interaction parameters demonstrate that for intact molecules (deprotonation level (DPL) = 0) the energy of the HON structure is always lower than that of the O phase. With an increase of DPL, the difference between the energies of these two structures decreases: while for DPL = 0.5, the possibilities to obtain the HON or O phase are very similar, for DPL = 1 the O phase has a higher probability to exist in comparison to the HON phase.

Halogenated Anthracenes as Building Blocks for the On-Surface Synthesis of Covalent Polymers: Structure Prediction with the Lattice Monte Carlo Method

“…In those instances, it has been possible to establish the structure–property relationship between a molecular building block and the resulting assembly and to identify basic molecular features responsible for the formation of a given superstructure. In this field, methods such as molecular dynamics − and Monte Carlo simulations − have been used most frequently. The latter method, especially in its coarse-grained variant, revealed to be a powerful tool that allowed for the fast and correct prediction of adsorbed superstructures, including molecular networks, , strings, cyclic oligomers, , fractal aggregates, , and others. , The MC method has also been used to study metal–organic systems on surfaces, demonstrating the possibility of steering the self-assembly by manipulating intrinsic properties of contributing molecules. ,− …”

“…In this field, methods such as molecular dynamics − and Monte Carlo simulations − have been used most frequently. The latter method, especially in its coarse-grained variant, revealed to be a powerful tool that allowed for the fast and correct prediction of adsorbed superstructures, including molecular networks, , strings, cyclic oligomers, , fractal aggregates, , and others. , The MC method has also been used to study metal–organic systems on surfaces, demonstrating the possibility of steering the self-assembly by manipulating intrinsic properties of contributing molecules. ,− …”

“…The latter method, especially in its coarse-grained variant, revealed to be a powerful tool that allowed for the fast and correct prediction of adsorbed superstructures, including molecular networks, 38,39 strings, 39 cyclic oligomers, 42,43 fractal aggregates, 42,43 and others. 36,38 The MC method has also been used to study metal−organic systems on surfaces, demonstrating the possibility of steering the self-assembly by manipulating intrinsic properties of contributing molecules. 39,42−44 Recently, we proposed the coarse-grained MC model of the self-assembly of metal−organic precursor structures of the Ullmann-type reaction comprising naphthalene (n) monomers with differently positioned halogen atoms.…”

Modeling of High-Temperature Ordered Structures with Weak Intermolecular C–H···F and C–H···N Bonds

“…The applications of MC modeling are not limited only to the research of systems of neutral (intact) molecules. Calculations were also carried out to investigate the mixtures of intact and partially deprotonated organic molecules, − as well as to simulate assembly of fully deprotonated molecules, , possessing carboxylate groups and bonded by classical and ionic HBs, corresponding to high-temperature annealing and electric field effect.…”

Variation of interaction zone size for the target design of 2D supramolecular networks

“…Computer simulations can give valuable insight for experimentalists due to the possibility of examination of the influence of multiple factors, such as particle geometry, under different conditions on the self-assembly process in a reasonable time. The most popular methods involve quantum density functional theory, 20 classical Monte Carlo [21][22][23][24][25][26] and molecular dynamics simulations (MD). 27,28 In our laboratory, we have proven that the last method can be useful for examination of a variety of molecular geometries, both in one-component systems 29,30 and in binary mixtures.…”