(189co) Using Free Energy Perturbation (FEP) to Rank Binding Affinities for ssDNA-Wrapped Single-Walled Carbon Nanotube (SWCNTs)

Separating and purifying single-walled carbon nanotubes (SWCNTs) is a challenge which currently inhibits their widespread application in fields that harness their unique electrical and optical properties. A novel strategy that has recently emerged for separating single-walled carbon nanotubes (SWCNTs) by chirality is the use of aqueous two-phase extraction (ATPE) in conjunction with single-stranded DNA (ssDNA) as a dispersant. This technique 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 are currently searched by costly trial and error. In this talk, we describe a new protocol using molecular simulations and free energy perturbation (FEP) that can be used to quantify and rank the binding affinity of ssDNA-SWCNT pairs based on differences in their free energy of solvation. To test the method, we study the ssDNA-SWCNT binding process for both optimal and non-matching binding pairs and find that the ranking of ssDNA sequence binding affinity relative to specific SWCNT chiralities matches very well with experimental observations. We also study the effect of the relative concentration of ssDNA and use that information to quantify the effect of inter- and intra-strand ssDNA hybridization on the free-energy – yielding insight into the physics that drive the stability of the binding process. Future work to use the new protocol to design optimal binding pairs will also be described.