The fact that YY + , 5 + , and O + had residence times similar to those of neutral molecules implies that the molecules preferentially associated with the ssDNA-SWCNT conjugate than the SWCNT surface for majority of the simulation. However, unlike the other positively charged molecules, their binding interactions were less stable, which led to shorter residence times. Importantly, these analyses reveal that binding does not predict an analyte's ability to elicit an optical response, as is evident from the binding results of YY+, which elicited no optical response in experimental measurements, but exhibits robust binding behavior in MD simulations (Figure ).