Symmetry breaking in covalent organic frameworks (COFs) lowers the energy and increases the valence to conduction band separation of the material.

The local structures of layered covalent-organic frameworks (COFs) deviate from the average crystal structures assigned from X-ray diffraction experiments. For two prototype COFs of Tp-Azo and DAAQ-TFP, density functional theory calculations have shown that the eclipsed structure is not an energy minimum and that the internal energy is lowered for an inclined stacking arrangement. Here we explore the structural disorder of these frameworks at 300 K through molecular dynamics (MD) simulations using an on-the-fly machine learning force field (MLFF). We find that an initially eclipsed stacking mode spontaneously distorts to form a zigzag configuration that lowers the free energy of the crystal. The simulated diffraction patterns show good agreement with experimental observations. The dynamic disorder from the MLFF MD trajectories is found to persist in mesoscale MD simulations of 155 thousand atoms, giving further confidence in our conclusions. Our simulations show that the stacking behaviour of layered COFs is more complicated than previously understood.