Monolayer protected metal clusters comprise a rich class of molecular systems and are promising candidate materials for a variety of applications. While a growing number of protected nanoclusters have been synthesized and characterized in crystalline forms, their dynamical behavior in solution, including prenucleation cluster formation, is not well understood due to limitations both in characterization and first-principles modeling techniques. Recent advancements in machine-learned interatomic potentials are rapidly enabling the study of complex interactions such as dynamical behavior and reactivity on the nanoscale. Here, we develop an Au-S-C-H atomic cluster expansion (ACE) interatomic potential for efficient and accurate molecular dynamics simulations of thiolate-protected gold nanoclusters (Au_n(SCH₃)_m). Trained on more than 30,000 density functional theory calculations of gold nanoclusters, the interatomic potential exhibits ab initio level accuracy in energies and forces and replicates nanocluster dynamics including thermal vibration and chiral inversion. Long dynamics simulations (up to 0.1 μs time scale) reveal a mechanism explaining the thermal instability of neutral Au₂₅(SR)₁₈ clusters. Specifically, we observe multiple stages of isomerization of the Au₂₅(SR)₁₈ cluster, including a chiral isomer. Additionally, we simulate coalescence of two Au₂₅(SR)₁₈ clusters and observe series of clusters where the formation mechanisms are critically mediated by ligand exchange in the form of [Au-S]_n rings.