In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we present results for the thermodynamics and dynamics of one of these clusters (NaCl)(35)Cl-. As the time scales for the structural transitions can be much longer than those accessible by conventional dynamics simulations, we use a master equation to describe the probability flow within a large sample of potential energy minima. We characterize the processes contributing to probability flow between the different nanocrystals, and obtain rate constants and activation energies for comparison with the experimental values.