Computational Study of the Molecular Mechanisms in two-dimensional Organic Frameworks for Chemical Applications

Abstract

2-Dimensional Metal Organic Frameworks(MOF) and Covalent Organic Frameworks(COF) have emerged as important candidates for diverse chemical applications such as molecular and bio- catalysts, single-ion conductors etc. In this study, we investigate the molecular mechanisms underpinning the stabilization of a 2D-MOF5 nanocrystal and conduction in a TpBd-based COF. In this thesis, we study chemical systems through a multiscale approach, combining the tools of Atomistic Molecular Dynamics(MD) and Density Functional Theory(DFT), to understand precise mechanisms and their physical principles in highly-periodic organic frameworks. We investigate a crystal lattice-guided etching of a 2D MOF-5 nanocrystal, which resulted in two distinct anisotropic pore patterns: plus(+)-shaped and fractal-patterned pores via <100> and <110> directional etching, respectively. We identified a two-step mechanism - the exchange of metal- coordinating solvent molecules with EtOH, and then the dissolution of EtOH-bound Zn-nodes. The thermodynamically preferred pathway proceeded through dissociation of Zn nodes in <100>- direction, while the slow-diffusion limited kinetic pathway was induced by faster solvent exchange in <110>-direction. Based on this mechanism, the etching process has been optimized to yield superb catalytic activity with long-term stability, offering strategies for the creation of custom patterns on 2D nanomaterials to address new scientific challenges. In a TpBd-based COF structure, designed to function as a single Li-ion conductor, we focused on identifying distinct molecular conduction pathways, and studying in detail the factors influencing the performance of the device. We have also studied the molecular interactions between the COF and the conducting ions, to fully understand and guide the preparation of such materials for energy applications. The goal of our work is to demonstrate the value of multiscale molecular simulations in studying various aspects such as formation and conduction in chemical systems like highly ordered organic frameworks. We clearly establish the methods of analysis and strategies that can guide the development of such materials for scientific applications.