Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of...

Molecular dynamics simulations were used to characterize the self-assembly of single-stranded DNA (ssDNA) on a (6,5) single-walled carbon nanotube (SWCNT) in aqueous solution for the purpose of gaining an improved theoretical understanding of separation strategies for SWCNTs using ssDNA as a dispersant. Four separate ssDNA sequences, ((TAT)₄, TTA(TAT)₂ATT, C₁₂, (GTC)₂GT), at various levels of loading, were chosen for study based on published experimental work showing selective extraction of particular SWCNT species based on the ssDNA dispersant sequence. We develop a unique workflow based on free energy perturbation (FEP) and use this to determine the relative solubility of these complexes due to the adsorption of the ssDNA on the SWCNT surface, and hence, rank the favorability of separations observed during experiments. Results qualitatively agree with experiments and indicate that the nucleobase sequence of the adsorbed ssDNA greatly affects the free energy of complex solvation which ultimately drives SWCNT separation. Further, to elucidate the underlying physics governing the ssDNA-SWCNT solubility rankings, we also present calculations for four structural characteristics of ssDNA adsorption. We demonstrate that a unique type of intra-strand hydrogen bonding is the most important factor contributing to the stability of the ssDNA-SWCNT complexes and show how these adsorption characteristics are coupled with the FEP results.