Despite the great success in achieving monodispersity for a great number of monolayer-protected clusters, to date little is known about the dynamics of these ultra-small metal systems, their decomposition mechanisms, and the energy that separates their structural isomers. In this work, we use density functional theory (DFT) to calculate and compare the ground state energy and the Born-Oppenheimer molecular dynamics of two well-known Au 38 (SCH 2 CH 2 Ph) 24 nanocluster isomers. The aim is to shed light on the energy difference between the two clusters isomers and analyze their decomposition mechanisms triggered by high temperatures. The results demonstrate that the energy that separates the two isomers is of the same order of magnitude as the energy difference between the fcc and hcp phases of bulk gold reported earlier. Moreover, the MD simulations show disordering and eventual fragmentation of the cluster structures at high temperature which seem to proceed via spontaneous formation of Au x (SR) y polymeric chains. Hence, these results greatly contribute to understanding the possible decomposition mechanism, stability and robustness of existing and new monolayer-protected clusters.