(70e) Solvation of Self-Assembled Complexes: Using Molecular Simulations to Probe Energetics, Structure, and Dynamics

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 size, chirality, and handedness 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 apply other approaches such as aqueous two phase extraction (ATPE) or ion-exchange chromatography (IEX) to sort the dispersed SWCNTs by their physiochemical properties. Single-stranded DNA (ssDNA) is a very effective dispersant that shows sequence-specific behavior during separation. 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 pairs must be searched by trial and error. In this study, we use replica exchange molecular dynamics (REMD) simulations to assemble the ssDNA-SWCNT complexes and then apply free energy perturbation methods to obtain an estimate for the solvation energy of the complex. Such systems require the construction of a novel free energy pathway to access the quantity of interest. Additionally, the structure and dynamics of the hydrating water has been analyzed to better understand the solvation behavior on a molecular level and to provide insight into the effects of ssDNA sequence. These investigations work towards our goal to provide better insight into the sequence/chirality specific separation mechanism, and to eventually develop a model that allows for the prediction of other pairs leading to the efficient sorting of a desired nanotube chirality.