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

Abstract

The self-assembly of a hydrogen bond “donor–acceptor” system with fluorinated pyridyl groups is considered to study the emergence of different ordered structures bonded by weak C–H···F and C–H···N bonds. We model the ordering of 4,4′-bis­(2,6-difluoropyridin-4-yl)-1,1′-biphenyl (BDFPBP) as a typical example of this type of linear molecules. BDFPBP on Au(111) is known to assemble into four molecular arrangements: a herringbone phase at room temperature and three other structures at 450–460 K. In our model, we assume partial deprotonation of donor sites in phenyl and pyridyl rings during heating. Therefore, as representatives of the BDFPBP molecular system at higher temperatures, we choose seven types of molecules (one intact and six with differently damaged donor sites) and suggest the mechanisms of their bonding. Using density functional theory, we estimate the energies of different hydrogen-bonding motifs for intact and damaged molecules. We also perform Monte Carlo simulations for homo- and bimolecular ensembles to obtain all experimentally observed molecular phases. In addition, we reveal several new structures and their coexistences with the phases known from experiments.

Theoretical Modeling of the Metal‐Organic Precursors of Anthracene‐Based Covalent Networks on Surfaces

“…Computer simulations of metal-organic adsorbed overlayers have been recently successfully used to predict outcomes of the self-assembly of various organic linkers. [28][29][30][31][32][33][34] In those instances simplified coarse-grained models of the self-assembling molecules and adsorbing surfaces have been proposed, resulting in a good agreement with the experiment. Moreover, new molecular architectures have been theoretically predicted (e. g. the Sierpiński triangle fractals [29] ) the formation of which was later confirmed experimentally.…”

“…Computer simulations of metal‐organic adsorbed overlayers have been recently successfully used to predict outcomes of the self‐assembly of various organic linkers [28–34] . In those instances simplified coarse‐grained models of the self‐assembling molecules and adsorbing surfaces have been proposed, resulting in a good agreement with the experiment.…”

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

“…Computational modelling of similar supramolecular systems is often employed to aid the experiments, especially for molecules engaging in multiple weak bonds. The nature of mixed X•••X and X•••H interactions between molecules in experimentally observed molecular arrangements can be revealed by density functional theory (DFT) calculations, which also provide the geometry associated with the ground state energy [17,18].…”

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.…”