Self-assembly of trimesic acid (TMA) molecules into the honeycomb structure with filled pores and the resulting host–guest chemistry are studied by the density functional theory (DFT) and Monte Carlo (MC) simulations. The DFT calculations demonstrate that a guest TMA molecule prefers a noncentral position in a relaxed hexagonal pore formed of six TMA molecules, and it is binded by two intermolecular interactions. The symmetric central position of the guest molecule is energetically favorable only in the honeycomb structure, which is compressed by more than 3%. Based on the estimated host–guest dimeric interactions, a model is proposed to identify the conditions for central and noncentral positioning of TMA molecules within the pore during their ordering into the honeycomb structure with partly filled pores. The MC simulations reveal that increase of the molecule–substrate interaction in the center of the pore or interactions of the central molecule with the cage molecules have a significant effect in preserving the central position of the guest molecule. However, if these interactions are not too strong, the noncentral position is favored due to multiplicity of noncentral arrangements in a hexagonal cage.
The nearest neighbor model is proposed to explain the occurrence of the metalassisted pinwheel structures of deprotonated trimesic acid molecules on Ag(111). The main bonding interactions of molecules in these structures are estimated by the density functional theory calculations. The determined interaction energies are further used as a starting point for Monte Carlo simulations performed for a broad range of interaction parameters and different deprotonation levels of molecules. In this paper, we use the molecular engineering approach by selecting the sets of molecules with different deprotonation levels to obtain the structures similar to those observed experimentally. For a large number of once-deprotonated molecules, we obtain a discrete pinwheel phase, PW1, which can also coexist with the knitted pinwheel structure, PW2, if completely deprotonated molecules participate in the self-assembly. The PW1 phase could also be formed of twice-deprotonated molecules, and coexistence of this phase with the PW2 structure is possible for strong binding intermolecular interactions. We demonstrate domains of different enantiomers occurring in the PW1 and PW2 structures.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.