(673b) Using Replica Exchange Molecular Dynamics Simulations to Examine Sequence Specificity in the Adsorption of Single-Stranded DNA (ssDNA) on Chiral Single-Walled Carbon Nanotubes (SWCNTs)

Single walled-carbon nanotubes (SWCNTs) possess unique properties that make them attractive for a number of applications. However, the difficulty in obtaining uniform samples in terms of chirality inhibits their widespread use. Various separation techniques address this problem through use of surfactants in order to suspend the tubes in aqueous media and then applying other approaches such as aqueous two phase extraction (ATPE) or ion-exchange chromatography (IEX) to sort the SWCNTs by their physiochemical properties. Single-stranded DNA (ssDNA) is a very effective dispersant that shows sequence-specific binding behavior. Previous experimental work has shown that this specificity can be harnessed to tune the separation in favor of particular nanotube chiralities. Currently, the nature of this specificity is not yet well understood and optimal ssDNA/SWCNT bindings must be searched by trial and error. In this study, we use replica exchange molecular dynamics (REMD) simulations to study and compare the binding of experimentally determined optimal and unfavorable binding pairs. We intend to compare the effect and interplay between a number of proposed binding factors including inter- and intra-strand interactions of the ssDNA, the ratio of Kuhn length to tube diameter, and the ssDNA equilibrium conformation relative to the chiral angle of the SWCNT. From these analyses our goal is to provide better insight into the sequence/chirality specific binding mechanism, and eventually to develop a model that allows for the prediction of other pairs leading to the efficient sorting of a desired nanotube chirality.