Reactive Force Field-Based Molecular Dynamics Simulations on the Thermal Stability of Trimesic Acid on Graphene: Implications for the Design of Supramolecular Networks

Abstract

In this work, we used the ReaxFF force field to investigate the dynamics of different network structures of trimesic acid (TMA) molecules on graphene as a function of temperature. We considered the so-called honeycomb, filled honeycomb, flower, zigzag, and close-packed TMA motifs. The thermal stability was investigated using molecular dynamics simulations with the constant number of molecules, volume, and temperature and force-biased Monte Carlo calculations up to 650 K. Our simulations provide detailed atomistic insights into the intermolecular and molecule−substrate interactions responsible for the self-assembly or the breakage of the TMA networks at different temperatures. The dynamics of hydrogen bonding were followed by counting the number of hydrogen bonds as well as by analyzing OH radial distribution functions. According to the melting temperatures obtained, the honeycomb structure has a higher stability than the high-coverage zigzag and close-packed structures. Guest TMA molecules within the pores of the honeycomb motif further increase its thermal stability, thus showing the beneficial effect of host−guest interactions. The twisting and rotation of carboxylic groups with increasing temperature are responsible for the breakage of hydrogen bonds, which ultimately leads to the melting of the networks. Partial TMA desorption observed at the onset of network disordering was attributed to the intermolecular vibrational energy transfer between the molecules. For the high-coverage close-packed network and for an island of TMA molecules with a close-packed structure, we observed a phase transition to the honeycomb structure as a consequence of the stronger dimeric −COOH bonding of the latter. The energetics of the formation of the different networks from TMA molecules in the gas phase was also investigated. Intermolecular interactions and TMA−graphene interactions have similar magnitudes. The stability of the different networks cannot be fully understood only based on energetic considerations, and in the case of the dense close-packed structure, MD simulations show how it is rapidly destabilized.

Thermodynamics of self-assembled molecular layers of trimesic acid from fields-supported kinetic Monte Carlo simulation

“…These values were adjusted to reproduce potentials of molecules in the CW, flower, and superflower (close-packed) structures of TMA layer on graphite obtained with the molecular dynamics and the density functional theory (DFT). 47 Parameters ε / k and r 0 were taken from our previous paper 18 as 360 K and 0.7588 nm, respectively.…”

“…Quantum chemical and molecular dynamics studies of atomistic models are mainly aimed at determining the energy of epitaxial growth of the TMA phases, assessing their relative thermal stability and disassembly mechanism. [44][45][46][47] In those works it was found that the most stable are the chicken-wire (CW) and filled CW structures. The filled CW structure contains an additional TMA molecule adsorbed in the centre of each hexagon formed by TMA molecules.…”

“…The filled CW structure contains an additional TMA molecule adsorbed in the centre of each hexagon formed by TMA molecules. According to various publications, these phases disassemble at temperatures of 300–400 K. In the paper of Jacquelin et al 47 the CW, filled CW, flower, zigzag, and close-packed TMA phases adsorbed on graphite were studied in detail by a molecular dynamics simulation. The authors showed that the destruction of the phase occurs due to twisting and rotation of carboxylic groups with increasing temperature.…”

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

“…Density functional theory (DFT) methods are often used to determine the possible geometries and energies of interactions in supramolecular networks. − Molecular dynamics and Monte Carlo (MC) modeling has been performed to find the most stable phases of triangular, ,− linear, cross-shaped, V-shaped, and other , molecules with various functional groups.…”

Minor adjustments in the chemical structures of pyridine derivatives induced different co-assemblies by O–H⋯N hydrogen bonds

“…7 A variety of structural transformations from a simple structure to a complex multicomponent structure have been reported in the past few decades. 8 Because of the stronger selectivity and directionality of hydrogen bond, the carboxylic acid-based nanostructures were formed at the interface and many external environmental factors, such as temperature, 9 concentration, 10 electric field, 11 and solvent, 12 were also imposed to regulate the original selfassembly. Except for the mentioned external environmental factors, introducing various adsorbates, such as carboxylic acid, 13 and pyridine derivatives 14 into the original acid-based self-assembly system could also construct varied co-assembly structures by breaking the original O-HÁ Á ÁO hydrogen bond and forming new non-covalent interactions.…”