Synthesis of [(MeCyt)2H]I-structure and stability of a dimeric threefold hydrogen-bonded 1-methylcytosinium 1-methylcytosine cation

Reaction of trimethylsilyl-protected cytosine with methyl iodide afforded N1-methylated product. Subsequent treatment with ethanol resulted in cleavage of the protection group forming [(MeCyt)2H]I (4). Identity of was confirmed by microanalysis, mass spectrometry, 1H and 13C NMR spectroscopy and by single-crystal X-ray diffraction analysis. Crystals of consist of dimeric [(MeCyt)2H]+ cations and I- anions. These ions are arranged in the crystal such that there is a strong base stacking (mean stacking distance 3,467 angstroms) and, furthermore, pi interactions between I- and cytosine rings (mean distance 3,737 angstroms). The dimeric [(MeCyt)2H]+ cations are centrosymmetric having three strong hydrogen bonds, namely two terminal N4-H...O' ones (N4...O' 2.815(4) angstroms) and a central N3-H...N3' (N3...N3' 2.813(4) angstroms) one. Quantum chemical calculations on the DFT level of theory show that the gas phase structure of the dimeric cation exhibits two different terminal N-HO hydrogen bonds, a stronger (N4...O' 2.722 angstroms) and a weaker one (N4'...O 2.960 angstroms). The central N3-HN3[prime or minute] hydrogen bond (N3...N3' 2.852 angstroms) was characterized to have an unsymmetrically located proton and a typical double minimum potential with a very low activation barrier. The interaction energy between [(MeCyt)H]+ and MeCyt yielding [(MeCyt)2H]+ was calculated to be -42.4 kcal mol(-1)(ZPE and BSSE corrected). Comparison with the interaction energy (calculated on the same level of the theory) between cytosine and guanine yielding the triply hydrogen-bonded Watson-Crick dimer (-24.2 kcal mol(-1)) revealed a much higher stability of the hydrogen bonds in [(MeCyt)2H]+.