Experimental and theoretical study of thymine and cytosine derivatives: the crucial role of weak noncovalent interactions

In this paper we report the synthesis of N-1-hexylthymine (1), N-1-hexylcytosine (2), N-1-hexylcytosine hydrobromide (3) and [(N-1-hexylcytosinium)center dot(N-1-hexylcytosine)](2)center dot[Cl2Hg(mu-Cl)(2)HgCl2] (4) (the hemiprotonated form of the N-1-hexylcytosine forming a CHC+ pair with carbonyl-amino symmetric and N-3-N-3 recognitions) and X-ray characterization of compounds 1, 3 and 4. In the solid state, N-1-hexylthymine 1 follows exactly the same behaviour as N-1-hexyluracil. In addition to strong hydrogen bonding interactions, various weak forces, i.e. C-H/pi, carbonyl-carbonyl (C=O center dot center dot center dot C=O) and anion-pi interactions (between the bromide and N-1 of cytosine in 3), play a key role in stabilizing the 3D architectures of the compounds. The theoretical calculations allow estimation of the strength of these contacts and how they influence each other.