On modeling biomolecular-surface nonbonded interactions: application to nucleobase adsorption on single-wall carbon nanotube surfaces.

In this work we explored the selectivity of single nucleobases towards adsorption on chiral single-wall carbon nanotubes (SWCNTs) by density functional theory calculations. Specifically, the adsorption of molecular models of guanine (G), adenine (A), thymine (T), and cytosine (C), as well as of AT and GC Watson-Crick (WC) base pairs on chiral SWCNT C(6, 5), C(9, 1) and C(8, 3) model structures, was analyzed in detail. The importance of correcting the exchange-correlation functional for London dispersion was clearly demonstrated, yet limitations in modeling such interactions by considering the SWCNT as a molecular model may mask subtle effects in a molecular-macroscopic material system. The trend in the calculated adsorption energies of the nucleobases on same diameter C(6, 5) and C(9, 1) SWCNT surfaces, i.e., G > A > T > C, was consistent with related computations and experimental work on graphitic surfaces, however contradicting experimental data on the adsorption of single-strand short homo-oligonucleotides on SWCNTs that demonstrated a trend of G > C > A > T (Albertorio et al 2009 Nanotechnology 20 395101). A possible role of electrostatic interactions in this case was partially captured by applying the effective fragment potential method, emphasizing that the interplay of the various contributions in modeling nonbonded interactions is complicated by theoretical limitations. Finally, because the calculated adsorption energies for Watson-Crick base pairs have shown little effect upon adsorption of the base pair farther from the surface, the results on SWCNT sorting by salmon genomic DNA could be indicative of partial unfolding of the double helix upon adsorption on the SWCNT surface.

Understanding effects of molecular adsorption at a single-wall boron nitride nanotube interface from density functional theory calculations.

In this paper, we explored computationally the feasibility of modulating the bandgap in a single-wall BN nanotube (BNNT) upon noncovalent adsorption of organic molecules, combined with the application of a transverse electric field. Effects of analytes' physisorption on the surface of BNNTs regarding structural and electronic properties were delineated. Relatively large binding energies were calculated, however, with minimal perturbation of the structural framework. Electronic structure calculations indicated that the bandgap of BNNTs can be modified by weak adsorption due to the presence of adsorbate states in the gap of the host system. Furthermore, we have shown that the application of a transverse electric field can tune the bandgap by shifting adsorbate states, consistent with calculated current-voltage characteristics.