Skip to main content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.


The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of ssDNA-Wrapped Single-Walled Carbon Nanotubes



Kevin R. Hinkle, Frederick R. Phelan Jr.


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 on the basis of 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 intrastrand 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.
Journal of Physical Chemistry C


Solvation Free Energy, Colloidal Adsorption, Solubility, Free-Energy Perturbation (FEP), Replica Exchange Molecular Dynamics (REMD), Single-Walled Carbon Nanotubes (SWCNTs), Single-Strand DNA (ssDNA), SWCNT Separations
Created June 4, 2020