Using molecular dynamics simulations, the structural properties and vibrational behavior of single- and double-walled carbon nanotubes (CNTs) under physical adsorption (functionalization) of Flavin Mononucleotide (FMN) biomolecule are analyzed and the effects of different boundary conditions, the weight percentage of FMN, radius and number of walls on the natural frequency are investigated. As the functionalized nanotubes mainly operate in aqueous environment, two different simulation environments, i.e. vacuum and aqueous environments, are considered. Considering the structural properties, increasing the weight percentage of FMN biomolecules results in linearly increasing the gyration radius. Also, it is observed that presence of water molecules expands the distribution of FMN molecules wrapped around CNTs compared to that of FMN molecules in vacuum. It is demonstrated that functionalization reduces the frequency of CNTs, depending on their boundary conditions in vacuum which is more considerable for fully clamped (CC) boundary conditions. Performing the simulations in aqueous environments demonstrates that, in the case of clamped-free (CF) boundary conditions, the frequency increases unlike that of CNTs with fully clamped and fully simply supported boundary conditions. The value of frequency shift increases by rising the weight percentage of FMN biomolecule. Moreover, it is observed that the frequency shifts of SWCNTs with bigger radius are more considerable, whereas the sensitivity of frequency shift to the weight percentage of FMN biomolecule reduces and this is more pronounced as the simulation environment is aqueous.