We further explored whether "perturbation cross sections" of analytes are influenced by the proximity of polar functional groups of the analytes close to nanotube surfaces. This exploration was motivated by previous studies demonstrating that the dielectric constant of the nanotube's environment significantly impacts SWCNT photophysics. For example, Silvera-Batista and colleagues showed that increasing the dielectric constant of SWCNT environment from 2 to 5 by changing solvents could reduce the photoluminescence intensity by more than 50%. Building on these findings, we investigated whether the polar functional groups of each analyte, when in close proximity to the nanotube surface, could perturb the electrostatic field around the ssDNA-SWCNTs and thus influence their optical properties. Towards this goal, we measured the distances between the center of mass (COM) of each analyte's polar functional groups and the nanotube surface in all MD simulations, focusing on trajectory frames in which the groups were found within 10.0 Å of the nanotube surface. The observed distances were then used to generate probability distributions of the distances between analyte polar groups and SWCNT surfaces (Fig. ). For instance, the molecule F + has two polar functional groups: -OH and -NH3 + . An examination of its probability distribution shows that hydroxyl groups have a high probability of being within 3.0-4.0 Å away from the SWCNT surface, whereas the protonated amine has a peak at ~ 5.2 Å away from the nanotube surface. In contrast, the neutral molecule F showed similar distance distributions for its hydroxyl groups, but the amine group was closer to the nanotube surface, with a maximum at 3.5 Å. This data is consistent with the analyte binding modes discussed earlier, where F + molecules exhibiting an insertion mode of binding, with the protonated amine sometimes projecting away from the nanotube surface. On the other hand, F molecules tended to stack on the ssDNA corona or the nanotube surface, with both the -OH and -NH2 groups at similar distances from the surface. DA + molecules were observed to lie flat on the nanotube surface, but the protonated amine group, located two carbon centers away from the aryl ring, projected upward and away from the nanotube surface, interacting with the negatively charged ssDNA. This binding observation is consistent with the polar group distribution profiles (Fig. ).