It is noteworthy that π-stacking is an anticipated binding mode for the molecules we studied, largely because a central feature of their molecular structure is an aryl group, which tends to stack on ssDNA bases and the graphitic lattice of SWCNTs. The binding modes we observed align with our previous computational work, where dopamine was shown to stack on surfaces of SWCNTs and ssDNA-SWCNTs. In this study, we further observed that the identity and positioning of functional groups around the central aryl motif influenced the preferred binding modes of the analytes. We attribute this to the fact that polar functional groups typically engage in directional interactions, and this influences the overall orientations of the analytes on nanotube surfaces. A common observation for analytes with positively charged -NH3 + groups (F + , DA + , YY + , RR + , O + , 5 + ) is their propensity to interact with the ssDNA phosphate backbone (fig. ). Among these, dopamine (DA + ) exhibited the strongest tendency to participate in this type of binding interaction. This directional interaction between the positively charged amine groups and negatively charged ssDNA phosphate backbone is a key factor determining the predominant binding modes in all the positively charged molecules. Since the protonation state of amine groups is pH-dependent, these findings help explain our experimental observation that pH is a critical extrinsic factor influencing fluorescence responses. ) and the negatively charged molecule (C -) exhibit transient binding behavior, making it difficult to identify the primary factors governing their binding behavior. A comparison of DA + and T binding to the SWCNT surface over time is shown in fig. . Despite the transient nature of these interactions, hydrogen bonds between the -OH or -NH2 functional groups and the oxygen atoms of the ssDNA sugar-phosphate backbone, or the nitrogen atoms of the ssDNA bases, are frequently observed (as seen, for example, in the binding pose for C shown in Fig. ). In summary, based on a visual inspection of the simulation trajectories, we hypothesize that the functional groups present in these analytes primarily dictate the preferred binding mode of ligands.