Modeling of Different Ordering Schemes for Halogen-Functionalized Molecules with Triazine and Benzene Core

Abstract

We propose a model based on pairwise intermolecular interactions explaining the occurrence of different structures in seemingly similar experiments of self-assembly of star-shaped 2,4,6-tris­(4-halophenyl)-1,3,5-triazine (TXPT = TBPT, TIPT with X = Br and I) on solid surfaces. The model is universal and could be extended to analogous polyaromatic compounds with benzene core. Density functional calculations reveal that two main interactions of this system have different origins but very similar magnitudes (e 1 ≈ e 2). This allows the formation of either e 1-bonded or e 2-bonded molecular ribbon-like structures. Along with the relation for the third main interaction, e 0 = 0.64e 1, we found two weaker complementary interactions and prepared the phase diagram of the TXPT system, which shows the domains of all four experimentally known structures in a tiny region of interaction parameters space. Using our model, we performed the ground-state analysis and extensive Monte Carlo simulations of the TXPT ensembles to substantiate our arguments. The results show that even a slight alteration in the balance of the main interactions leads to the self-assembly of different supramolecular networks. It is demonstrated that the row-like experimental phase may have several possible molecular arrangements with different bonding motifs and similar energies. The experimentally known coexistence of two phases is also reproduced in simulations.

Model for self-assembly of Br–H and Br–Br bonded Br4Py molecules

“…The larger system was mainly used for testing the finite size effects. We employ the Metropolis scheme with the non-local version of the Kawasaki dynamics algorithm as implemented in previous studies [17,23]. At each Metropolis step, we first calculate the initial pair interaction energy E i of a randomly selected molecule.…”

“…The collective behaviour of large molecular ensembles is usually studied using less accurate, but more efficient computational methods, such as Monte Carlo (MC) or molecular mechanics modelling. Such studies based on force fields or utilizing purposely built interaction models for treating the assembly of various small organic molecules have been published recently [9,[19][20][21][22][23][24].…”

Toward Molecular Fractals on Surfaces: Designing Covalent Structures with the Monte Carlo Simulation Method

“…Computer simulations based on theoretical methods have been a useful complementary approach to the self-assembly of functional molecules on surfaces, enabling easy manipulation of molecular parameters and tracing the evolution of the resulting superstructures. − As in laboratory practice, for each candidate building block (including the PAH derivatives), investigations of the self-assembled architectures require prior organic synthesis and subsequent scanning tunneling microscopy (STM) imaging; the associated computer simulations can be a valuable addition or alternative. Inspired by this possibility, to reduce experimental efforts associated with the screening of the set of candidate PAH building blocks, we recently proposed the lattice Monte Carlo (MC) model of the formation of labile metal–organic precursors of the Ullman coupling reaction running on a (111) catalytically active substrate.…”

Ordering of monomers, dimers and polymers of deposited Br2I2Py molecules: a modeling study

“…MC calculations can be performed very efficiently using purposely built interaction models which recently proved their successful ability to study the assembly behavior of various small organic molecules with hydrogen and halogen bonds. 21–25…”

“…MC calculations can be performed very efficiently using purposely built interaction models which recently proved their successful ability to study the assembly behavior of various small organic molecules with hydrogen and halogen bonds. [21][22][23][24][25] In this work, we present the model for ordering of Br 2 I 2 Py molecules in two-dimensional, dimeric and polymeric structures. Using DFT calculations, we estimate two pair interaction energies responsible for two-dimensional ordering of intact molecules.…”