N. Kurita et al., Density functional study for stacking energy of cytosine dimer: Ab initio MO calculations based on Slater-type basis set, INT J QUANT, 76(6), 2000, pp. 677-685
To clarify the efficiency of the molecular orbital (MO) method based on the
density functional theory (DET) for describing the stacking properties of
DNA bases, we have investigated the stacking energy of the cytosine dimer b
y using the Gaussian programs and our developed MO program based on DFT and
Slater-type basis set. The most remarkable finding is that our DFT method
can reproduce the dependence of stacking energy on stacking geometry obtain
ed by the ab initio second-order Moller-Plesset (MP2) method, whereas the D
FT methods in Gaussian fail to do so. This fact comes mainly from the diffe
rence in the types of basis sets, indicating that the Slater-type one is mo
re suitable for describing long-range interactions such as the DNA base sta
cking. The amounts of computational time and memory needed for our method a
re much smaller than those for the MP2 method. Therefore, our method may be
more efficient than the MP2 method and make it possible to investigate sta
ble structures and electronic properties of more realistic and large-sized
models for stacked DNA base pairs. (C) 2000 John Wiley & Sons, Inc.