Density functional study for stacking energy of cytosine dimer: Ab initio MO calculations based on Slater-type basis set
✍ Scribed by Noriyuki Kurita; Masahiro Araki; Kenji Nakao; Kinya Kobayashi
- Publisher
- John Wiley and Sons
- Year
- 2000
- Tongue
- English
- Weight
- 416 KB
- Volume
- 76
- Category
- Article
- ISSN
- 0020-7608
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✦ Synopsis
To clarify the efficiency of the molecular orbital (MO) method based on the density functional theory (DFT) for describing the stacking properties of DNA bases, we have investigated the stacking energy of the cytosine dimer by 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 obtained by the ab initio second-order Møller-Plesset (MP2) method, whereas the DFT methods in Gaussian fail to do so. This fact comes mainly from the difference in the types of basis sets, indicating that the Slater-type one is more suitable for describing long-range interactions such as the DNA base stacking. The amounts of computational time and memory needed for our method are 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 stable structures and electronic properties of more realistic and large-sized models for stacked DNA base pairs.