Molecular dynamics simulation of aspirin dissolution

Capturing Crystal Shape Evolution from Molecular Simulations

A simple and efficient algorithm for tracking shape evolution of small-molecule organic crystals during molecular simulations is described. It is based on the reconstruction of a crystal surface from molecular coordinates using an alpha-shape triangulation algorithm followed by the DBSCAN clustering of neighboring triangles with similar normal vectors to crystal faces. No information except the unit cell parameters is needed beforehand, enabling the user to automatically detect not only existing but also new forming crystal faces and edges, which is valuable for prediction of growth and dissolution kinetics. The results are demonstrated for aspirin and paracetamol crystals.