Modeling the Stability and the Motion of DNA Nucleobases on the Gold Surface

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Abstract
We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol(-1), and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considered.