Computational analysis of stacking interactions between 3-nitropyrrole and natural nucleobases.
The stacking energies between natural nucleobases and a universal base of 3-nitropyrrole (3-NP) were calculated by use of two theoretically independent quantum chemical methods, namely, molecular orbital (MO) and density function theory (DFT) calculations. The parameters required for molecular mechanics calculation of 3-NP were obtained by use of a software of Direct Force Field and used to evaluate the stacking energy of the complexes formed between 3-NP and canonical four nucleobases. Dependence of the twist angle between the two stacked bases on the stacking energy was studied in great detail.
Ukawa
Hisashi
H
Frontier Collaborative Research Center, Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
Seio
Kohji
K
Sekine
Mitsuo
M
D009711:Nucleotides / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D011789:Quantum Theory
D009711:Nucleotides; D011758:Pyrroles; C094911:3-nitropyrrole