We studied theoretically the interaction of simple aliphatic amines with carboxylated zigzag and armchair single-walled carbon nanotube (SWNT) models. We used single-level MM+ molecular mechanics and the AMI semiempirical method to study noncovalent interactions. To study the model amidation reaction with methylamine, the two-level ONIOM technique was employed in which the higher level was treated with B3LYP/6-31G(d) DFT, and the lower level was described with either universal force field (UFF) molecular mechanics or AMI. In the single-level calculations, the molecular mechanics strongly overestimated van der Waals interactions of amine molecules with the nanotube walls whereas totally ignored hydrogen bond formation between NH2 and COOH groups. On the contrary, AMI calculations produced unrealistic hydrogen-bonded structures where no attraction was manifested between the hydrophobic fragments. In the ONIOM calculations at the B3LYP/6-3lG(d):UFF level of theory, CH3 group of methylamine was strongly attracted to the nanotube, and its N-C bond was directed toward SWNT's center of mass in reaction complex, transition state, and product. Correspondingly, free rotation around C-C(=O)O bond was hampered, which resulted in the existence of two series of isomers, depending on where the methylamine moiety is located, inside or outside the nanotube cavity. At the B3LYP/6-3 I G(d):AM I level of theory, attraction between the hydrophobic moieties was very weak or absent, and both "inside" and "outside" starting geometries resulted in very similar reaction complexes, with the N-C bond of methylamine turned outward the nanotube. In addition to that, problems were found in the optimizations requiring force-constant calculations (transition states and vibrational frequencies). In all the ONIOM calculations, the formation of amide derivatives on carboxylated armchair SWNT tips was more energetically preferable than that on the zigzag nanotubes. In addition, in some cases of the "inside" zigzag isomers the reaction was endothermic, whereas it was always exothermic for their armchair models. To study theoretically chemical reactions on carbon nanotube tips by ONION! technique, where the higher level is treated with B3LYP density functional theory, we recommend UFF molecular mechanics versus the AM I semiempirical method for the lower-level description. To avoid artifacts associated with wall effects inside the, nanotube cavity (such as unrealistically long N-(HO)-O-... separations, which are supposed to be hydrogen bonds in reaction complexes), the use of nanotube diameters close to the commonly observed SWNT diameters is recommended.