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

Abstract

In this paper we report the synthesis of N¹-hexylthymine (1), N¹-hexylcytosine (2), N¹-hexylcytosine hydrobromide (3) and [(N¹-hexylcytosinium)·(N¹-hexylcytosine)]₂·[Cl₂Hg(μ-Cl)₂HgCl₂] (4) (the hemiprotonated form of the N¹-hexylcytosine forming a CHC⁺ pair with carbonyl-amino symmetric and N³–N³ recognitions) and X-ray characterization of compounds 1, 3 and 4. In the solid state, N¹-hexylthymine 1 follows exactly the same behaviour as N¹-hexyluracil. In addition to strong hydrogen bonding interactions, various weak forces, i.e. C–H/π, carbonyl–carbonyl (CO⋯CO) and anion–π interactions (between the bromide and N¹ 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.