RR+ has two polar groups: -NH2 and -NH3+. The neutral amine shows a moderate probability of being near the nanotube surface (maximum at 3.4 Å) and a higher probability of being farther away (maximum at 6.4 Å). In contrast, the protonated amine has a one large peak at 5.4 Å. For molecule RR with two neutral amine groups, the distribution is similar for both, with a maximum at 6.4 Å. For O + , the protonated amine is closer to the nanotube (maximum at 5.4 Å) than the neutral -OH group (maximum at 6.6 Å). In the neutral molecule O, the two polar groups have similar distribution. For C and C -, deprotonation of one of the ortho -OH groups in C results in a drastic rearrangement in distribution, with all polar groups in C -more than 6.0 Å away from the nanotube surface. Molecules Y, T, and 1 all exhibit a similar distribution pattern, with moderate probabilities at ~ 3.5 Å from the nanotube surface, and much higher probabilities farther away (~ 6.5 Å). Between the isomers T and 1, the -OH groups in 1 have slightly higher probability of being closer to the nanotube surface than those in T. For YY + molecules, the polar -NH3 + group is situated two carbon centers away from the indolamine. Consequently, stacking on the nanotube surface leads to the polar group being projected away from the nanotube surface, similar to the behavior of DA + molecules. A similar observation is noted for the -NH3 + group in 5 + . These findings provide understanding of how different analytes interact with the nanotube, placing an emphasis on the spatial distribution of polar functional groups relative to the nanotube surface.