Our interest in computation and modeling of biomolecules extends also to the study of nano-materials. A variety of chemically tunable reactions in metallic nanoparticles can be obtained by encapsulation of nanocrystals in alkanethiolate monolayers to form hybrid systems known as monolayer protected clusters (MPCs). Exploiting MPCs for applications in the area of catalysis requires a proper structural and dynamical characterization of the physical properties of the protecting layer. In particular, we are interested in MPCs that can bio-conjugate with proteins.