The elongation method was developed to calculate the local density of states (LDOS) at ab initio molecular orbital (MO) level. This method is performed on eight types of DNA molecules: namely, a pitch of A- and B- type poly(dA)A·poly(dT) and poly(dG)A·poly(dC), and they are neutralized by H+ and Na+, respectively. The difference of total energy between elongation and conventional calculations in each step is considerably small in the order of 10-9 hartree/atom for 20 units of B-type poly(dA)A·poly(dT) model. When the figures of total DOS of each model was compared, the energy gap of model containing Na+ is smaller than that of corresponding model containing H+. The LDOS for each model estimated by elongation method can well reproduce the results by conventional method. The LDOS figures show that the valence bands in A- and B-type DNA are formed by the highest occupied MOs (HOMOs) of adenine/guanine. Na+ can greatly decrease the energy of lowest unoccupied MO (LUMO) and consequently decrease the energy gap between LUMO and HOMO. The electron transfer between stacking adenine/guanine and sodium would play an important role in the conductivity of A- and B-type DNA.
All Science Journal Classification (ASJC) codes
- Atomic and Molecular Physics, and Optics
- Condensed Matter Physics
- Physical and Theoretical Chemistry