Theoretical study of the interaction between guanine and cytosine

Abstract

The interaction between guanine and cytosine has been studied using DFT method. The calculation includes the optimization of geometry of guanine, cytosine and their dimers at the B3LYP/6-311++G(d,p) level of theory. The optimized structures have been used to compute the binding energy at the B3LYP/6-311++G(3df,2p). The obtained result consists of nine cyclic dimers. All the dimers are stabilized by hydrogen bonds such as NH…N, NH…O, CH…N, CH…O. The GC2 dimer contains three hydrogen bonds, while other dimers are only comprised of two hydrogen bonds. The formation of the hydrogen bonds in the dimers results in the elongation of the NH and CH bonds and red shifts of the corresponding NH and CH stretching vibrations in eight dimers. The exception of a small blue shift of C5H2 bond is witnessed in the GC8 dimer. The prolongation of the bonds ranges between 0.002 and 0.028 A. Meanwhile, the contraction of the C5H2 bond is only 0.001 A. In addition, infrared intensities of the vibrations increase by the region of 0.03 to 3721 km mol⁻¹. The calculation predicted that the GC2 dimer is the most stable. Moreover, the GC2 dimer is also the G-C base pair in nature. The binding energy of the GC2 dimer is -22.71 kcal moi⁻¹. The value is in better agreement with the experiment than other previous studies.