Using Free Energy Perturbation to Differentiate ssDNA-Wrapped Single-Walled Carbon Nanotube Complexes*

The challenge of separating and purifying single-walled carbon nanotubes (SWCNTs) currently inhibits their widespread application in fields that harness their unique electrical and optical properties. Successful techniques involve dispersion in aqueous media before applying separation protocols such as aqueous two phase extraction to sort the dispersed SWCNTs by their physiochemical properties. Single-stranded DNA (ssDNA) is a very effective dispersant and displays sequence-specific behavior which allows one to tune the separation in favor of particular SWCNT chiralities. The nature of this specificity is not well understood and optimal ssDNA/SWCNT pairs must be searched by costly trial and error. We use molecular simulations and free energy perturbation (FEP) to quantify the differences in the various ssDNA-wrapping species in terms of both loading and sequence. Ultimately, it is our goal to provide insight into the sequence/chirality specific separation mechanism, and to develop a model that allows for more efficient design of the SWCNT purification process.