Noncovalent interactions of nucleic acid bases with fullerene C₆₀ and short carbon nanotube models: a dispersion-corrected DFT study

Abstract

In the present work, we studied theoretically the noncovalent interaction of six nucleobases (NBs), namely uracil (U), thymine (T), cytosine (C), 5-methylcytosine (m⁵C), adenine (A) and guanine (G), with fullerene C₆₀ and two closed-end SWNT models of armchair (ANT) and zigzag (ZNT) chirality. The calculations were performed using the functional PBE of general gradient approximation, empirical dispersion correction by Grimme, in conjunction with the DNP double numerical basis set. For comparison purposes, two sets of calculations were carried out: the first one, under vacuum conditions, and the second one, in aqueous medium. We analysed the computed geometries and binding energies for NB + CNC complexes, the plots of HOMO and LUMO orbitals and the values of corresponding HOMO-LUMO gap energies. In particular, we found that under vacuum conditions, the interaction strength decreases in the order of G > m⁵C > A > C > T > U for C₆₀ and ZNT, and G > A > m⁵C > C > T > U for ANT. In aqueous medium, the binding energies decrease in the order of G > A > m⁵C > T > C > U for C₆₀ and ANT, and G > A > T > m⁵C > C > U for ZNT.

Keywords:

• Nucleic acid bases
• fullerene C₆₀
• carbon nanotubes
• noncovalent interactions
• density functional theory
• dispersion-corrected calculations

Acknowledgements

A. A.S. appreciates the Master’s Degree Program in Biochemical Sciences of UNAM and CONACyT for M.Sc. fellowship.