Atomically precise ligand-protected nanoclusters (MPC) have emerged as an important class of molecules due to their unique structural features and diverse potential applications, including nano-electronics, bio-imaging, as sensors and drug carriers. Understanding the atomistic details of their intermolecular interaction is of paramount interest for designing, synthesizing, and system-specific applications. Crystal structures of various MPCs provide details related to molecular packing and intermolecular interactions. While these experiments reveal macroscopic, mostly static properties, they are often limited by the spatial and temporal resolutions in delineating the microscopic dynamical details. Here we apply molecular dynamics and enhanced sampling simulations to study the aggregation of Au25(pMBA)18 MPCs in the solution phase. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and periodic crystals. The free energy profiles obtained from enhanced sampling simulations of dimerization reveal a pivotal role of the protonated states of the ligands as well as the solvation shell in mediating the molecular aggregation process in solution. In the solid phase, the MPCs’ ligands have suppressed conformational flexibility owing to many facile intermolecular hydrogen bonds and π- stacks. Our work provides unprecedented molecular-level details of the aggregation process and conformational dynamics of MPCs ligands in the solution and crystalline phases, which will help rational design of new MPCs with specific properties.