The preferential binding of syn and anti configurational isomers of endo-functionalized bis-urea molecular receptor to 1,2-dinitrobenzene (G1) and 1,4-dioxane (G2) guests has been explained using dispersion-corrected M06-2X-based density functional theory. The host-guest binding is facilitated via hydrogen bonding, C-H center dot center dot center dot pi, dipole dipole, C center dot center dot center dot C and O center dot center dot center dot O (chalcogen-chalcogen) interactions. The formation of an inclusion complex is spontaneous and thermodynamically favorable. The molecular electrostatic potential and quantum theory of atoms in molecules in conjunction with the noncovalent interactions reduced density gradient have been employed to characterize the noncovalent interactions. The encapsulation of G1 or G2 within the pi- electron-rich cavity of the bis-urea macrocycle reflects the frequency shift of the characteristic N-H and C-H vibrations of their vibrational spectra. It has also been shown that binding of the bis-urea isomers to G1 and G2 emerges with a signature in the upfield signals of the guest protons confined to the host cavity in H-1 NMR spectra.