Simulation of the adsorption of nucleotide monophosphates on carbon nanotubes in aqueous solution

We use atomistic molecular dynamics simulations to calculate the binding energy of six different nucleotide monophosphates (NMPs) to a (6,0) single-wall carbon nanotube in aqueous solution. We examine two different aqueous environments, one with just two sodium counterions and a second consisting of approximately 134 mM sodium chloride solution. We find that the binding energies are generally favorable, of the order of a few kilocalories/mole. The binding energies of the different NMPs were very similar in salt solution, whereas we found a range of binding energies for NMPs in pure water. The binding energies are sensitive to the details of the association of the sodium ions with the phosphate groups and also to the average conformations of the nucleotides.