Characterizing Reaction Route Map of Realistic Molecular Reactions based on Weight Rank Clique Filtration of Persistent Homology

A reaction route map (RRM) constructed using GRRM program is a collection of elementary reaction pathways, each of which consists of two equilibrium (EQ) geometries and one transition-state (TS) geometry, connected by the intrinsic reaction coordinate (IRC). An RRM can be mathematically represented by a graph with weights assigned to both vertices, corresponding to EQs, and edges, corresponding to TSs, representing the corresponding energies. In this study, we propose a method to extract topological descriptors of a weighted graph representing an RRM based on persistent homology (PH). The work of Mirth et al. [J. Chem. Phys. 2021, 154, 114114], in which PH analysis was applied to the (3N-6)-dimensional potential energy surface of an N atomic system, is related to the present method, but the latter is practically applicable to realistic molecular reactions. The results of this study suggest that the descriptors obtained using the proposed method reflect the characteristics of the chemical reactions and/or physicochemical properties of the system accurately.Comment: 38 pages, 19 figure

On-water surface synthesis of crystalline, few-layer two-dimensional polymers assisted by surfactant monolayers

Despite rapid progress in recent years, it has remained challenging to prepare crystalline two-dimensional polymers. Here, we report the controlled synthesis of few-layer two-dimensional polyimide crystals on the surface of water through reaction between amine and anhydride monomers, assisted by surfactant monolayers. We obtained polymers with high crystallinity, thickness of ~2 nm and an average crystal domain size of ~3.5 μm2. The molecular structure of the materials, their grain boundaries and their edge structures were characterized using X-ray scattering and transmission electron microscopy techniques. These characterizations were supported by computations. The formation of crystalline polymers is attributed to the pre-organization of monomers at the water–surfactant interface. The surfactant, depending on its polar head, promoted the arrangement of the monomers—and in turn their polymerization—either horizontally or vertically with respect to the water surface. The latter was observed with a surfactant bearing a carboxylic acid group, which anchored amine monomers vertically through a condensation reaction. In both instances, micrometre-sized, few-layer two-dimensional polyamide crystals were grown