Molecular dynamics simulations are used to study the solvation and effective pair interactions of Au (1.2 nm) and CdSe (2.2 nm) nanoparticles passivated with alkanethiol and alkylamine ligands, respectively, for two different chain lengths in vacuum and n-hexane at 300 K. The solvation studies focus on quantifying the ligand and solvent shell structures, which are used to rationalize the interactions of nanoparticles in solution. To investigate the effective pair interactions, we compute the isotropic potential of mean forces (PMFs) between two nanoparticles and also analyze the anisotropy in the interactions that arises as a result of ligand shell fluctuations. Both isotropic and anisotropic contributions to the effective pair interactions between the two classes of nanoparticles are compared as a function of the ligand chain length and the solvent quality. It is demonstrated that the inclusion of the anisotropic aspect in the interparticle interactions is essential to properly describe the self-assembly thermodynamics of passivated nanoparticles. The implications of the coarse-grained modeling of the formation of binary nanocrystal superlattices (BNSLs) are considered.