DFT-based investigation of the electronic structure of a double-stranded AC B-DNA dimmer at different levels of theory.

Abstract

Calculations of the electronic structure of a stacked dimmer sequence from the D-(GCAAACGTTTGC)2 B-DNA dodecamer resolved in a PDB file 1HQ7 are performed within density functional theory. Seeking to understand the minimum level of theory that yields a reliable description for these systems, the basis sets 6-31g*, 6-31g*+BSSE, 6-311g*, 6-311g**, 6-311++g** along with the B3LYP and PBE0 exchange-correlation functionals were employed. These results are then used to implement a one-dimensional model of long stacked systems to obtain a new semi-empirical method that can be employed at low computational cost.