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Mercury detection due to harmful effects on the environment and human health is of importance. Among the reported methods, functionalized gold nanoparticles (AuNPs) due to their interesting ability for selective detection of Hg²⁺ have been considered. In this article, by employing full atomistic molecular dynamic (MD) simulations and quantum mechanic calculations, dynamical behavior and aggregation mechanism of the pure and 11-mecaptoundecanoic acid (MCA) functionalized gold nanoparticles (MCA-AuNPs) were investigated. MD simulation results indicate that pure AuNPs are not stable in water and aggregate due to van der Waals interactions. On the other hand, MCA groups increase the stability of AuNPs and their resistance against aggregation by elevating the repulsive interactions of the AuNPs. Moreover, MCA-AuNPs have the considerable ability for selective detection of Hg²⁺ in the presence of …