Density functional study for stacking energy of cytosine dimer: Ab initio MO calculations based on Slater-type basis set

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.