H-bonding interactions between simple DNA base cytosine and formamide molecules (model of protein unit): A density functional theory study

School of Chemistry and Chemical Engineering, Shandong University, Jinan 250 l 00, P. R. China

Department of Chemistry, Qufu Normal University, Shandong, Qufu 273165, P. R. China

E-mail: zhengyu@mail.qfnu.edu.cn

Manuscript received 5 May 2009, revised 31 A11gust 2009, accepted 7 September 2009

The molecular geometry of complexes C-F_n (n = 2-7) of cytosine with formamide molecules was calculated within the density functional theory using the B3LYP function at 6·31G(d) basis set level. It was found that the interaction with formamide molecules forming a locked chain around cytosine results in significant changes in its Intramolecular geometry. An obvious effect of hydrogen-bonding cooperativity can be seen during the complex process. The most Interesting geometrical change of cytosine upon the complex is the shortening of bond C4-N7 resulting from the strengthening of the conjugation between the 𝝅 system of the cytosine ring and the lone pair of the nitrogen atom. The significant elongation of C1-O8 bond and the presence or weak C-H •••O hydrogen bonds are also revealed.