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Understanding the Binding Mechanism of Various Chiral SWCNTs and ssDNA: A Computational Study
journal contribution
posted on 2012-12-27, 00:00 authored by Siamkhanthang Neihsial, Ganga Periyasamy, Pralok K. Samanta, Swapan K. PatiMolecular dynamics (MD) simulations have been carried
out to understand
the binding mechanism of various chiral single-walled carbon nanotubes
(SWCNTs) and single-stranded DNA (ssDNA) of four different nucleobase
sequences (i.e., ssdA14, ssdT14, ssdG14, and ssdC14, where, A, T, G, and C are adenine, thymine,
guanine, and cytosine, respectively) in aqueous media at room temperature
(300 K) and atmospheric pressure (1 atm). The simulations studies
reveal that ssDNA undergoes rapid structural changes and wrap around
the SWCNTs via π-stacking interactions between SWCNT’s
wall and the nucleobases of ssDNA. Our computations demonstrate that
the length of the ssDNA plays an important role during the wrapping
process. Moreover, it suggests that the length of the sequence should
be proportional to the diameter of the SWCNT, in order to overcome
the intralocked π-stacking interactions between the nucleobases
of ssDNA sequence. Also, in our classical MD simulation, we do not
observe the correlation between the diameter of SWCNTs and the sequences
of ssDNA, which indicates the importance of electronic factors of
these systems. In order to understand the electronic contributions
of these systems, the quantum calculations have been performed at
Hartree–Fock level for the 17 ns MD simulated structures. The
quantum chemical calculations provide evidence that the highly stable
ssDNA@SWCNT hybrid possesses a larger HOMO–LUMO gap.