Coronene Molecules in Hexagonal Pores of Tricarboxylic Acids: A Monte Carlo Study

Abstract

We propose a 7-state (orientation) model with some exclusions to describe the ordering of symmetry-reduced biphenyl-3,4',5-tricarboxylic acid (BHTC) molecules into planar ordered structures on a substrate lattice. The model is based on the 3-state Bell-Lavis model, which is used to describe the symmetric triangular molecules. The reduction of molecular symmetry allows us to predict different honeycomb-like structures H-bonded by dimeric and trimeric interactions. The model is supplemented by the guest-host interaction term which enables to analyze the effect of coronene on ordering of molecular structures. We find two structures formed by dimeric and trimeric interactions which can contain coronene in their pores and mix in different proportions depending on coronene concentration. The effect of host-coronene interaction on ordering of trimesic (TMA) and benzene-tribenzoic (BTB) acids is also studied using the -state Bell-Lavis model. We demonstrate that the interaction with coronene might induce the co-existence of coronene-filled honeycomb phase and coronene-free superflower phase in the TMA molecular system. We also predict that this interaction might induce the occurrence of superflower phase in the system of BTB molecules.

Theoretical Modeling of the Surface‐Guided Self‐Assembly of Functional Molecules

“…As the 2D nanoconfined self‐assembly/catalysis has been an emerging area in surface science, theoretical studies of the effect of nanoconfinement on the architecture of adsorbed molecular assemblies have been quite rare . These efforts, involving Monte Carlo(MC) and Molecular Dynamics calculations, have focused mainly on the capture and positioning of a single guest molecule (e. g. dicarbonitrile, coronene, trimesic acid, fullerene) inside pores of molecular template networks self‐assembled on graphite and metallic substrates . Very recently, Monte Carlo simulations were used to explore the self‐assembly of larger sets of linear molecules inside spacious triangular void spaces created on covalently modified graphite surface …”

“…[18] These efforts, involving Monte Carlo (MC) and Molecular Dynamics calculations, have focused mainly on the capture and positioning of a single guest molecule (e. g. dicarbonitrile, coronene, trimesic acid, fullerene) inside pores of molecular template networks self-assembled on graphite and metallic substrates. [18][19][20][21][22][23] Very recently, Monte Carlo simulations were used to explore the self-assembly of larger sets of linear molecules inside spacious triangular void spaces created on covalently modified graphite surface. [18] In this work, using the MC method, we examine how the nano-corrugation of a model surface can affect the outcome of the self-assembly of simple linear molecules with well-defined interaction centers.…”

Self-assembled monolayer formation of pentamers-like molecules onto FCC(111) surfaces: the case of curcuminoids onto Au(111) surface

“…Self-assembly of molecules with complicated chemical structure on a solid surface in most cases is determined by directional intermolecular interactions such as hydrogen bonding, dipole-dipole interactions, and coordination interactions. There are several papers on modeling of such systems using the lattice-gas model [48][49][50][51].…”

Modeling of the 2D self-assembly of tripod-shaped functional molecules with patchy interaction centers

“…The coarsegrained picture mentioned above has been frequently used in the Monte Carlo (MC) simulations of adsorbed systems on solid substrates. This refers to simple rod-like molecules (Matoz-Fernandez et al 2008;Centres and Ramirez-Pastor 2009;Nieckarz and Szabelski 2013) as well as to molecules with more complex structures, including cross-shaped units resembling porphyrins and phthalocyanines (Li and Lin 2011;Akimenko et al 2015;Kasperski et al 2015;Bischoff et al 2016;Gorbunov et al 2017), tripod-shaped tectons corresponding to tricarboxylic acid derivatives (Ibenskas and Tornau 2012;Misiunas and Tornau 2012;Šimenas et al 2015), dehydrobenzoannulenes (DBAs) (Szabelski et al 2010;Adisoejoso et al 2012) and molecules bearing pyridyl (Ciesielski et al 2013) and nitrile (Copie et al 2015) groups. The results from these theoretical studies demonstrate that the MC calculations, performed even for the simplified molecular representations, are able to reproduce correctly formation and coexistence of various adsorbed phases observed experimentally, especially the planar nanoporous networks observed either in ultra high vacuum or at the liquid/solid interface.…”

“…This situation refers to these adsorbed assemblies for which the corrugation of the surface-molecule potential results in a limited number of on-surface configurations of a single molecule and thus in the limited number of bimolecular connections differing in relative orientation/distance of the molecular partners. In consequence, often a constant number of intermolecular bonds (usually one or two) with fixed directionality that a single interaction center can provide is assumed in theoretical modeling (Ibenskas and Tornau 2012;Misiunas and Tornau 2012;Ciesielski et al 2013;Nieckarz and Szabelski 2014;Šimenas et al 2015;Szabelski et al 2016Szabelski et al , 2017. When, however, the molecular interaction centers (functional groups) are chemically more complex, for example being extended or flexible, the (maximum) number and directionality of intermolecular bonds can change when the molecules are allowed to adopt diverse adsorbed configurations.…”