Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmirn]Br (n=2, 4, 6, 8, 10) Microhydrates

The exploration of the ionic liquids' mechanism of action on nucleobase's structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([C(n)mim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH(2)O). Geometries of the mono-, di-, tri-, and tetraionic thymine (T-wH(2)O-y[C(n)mim](+)-xBr , w = 5-1 and x + y = 0 similar to 4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H(2)O-Br--1, T-3H(2)O-[C(n)mim](+)-Br-4, T-2H(2)O-[C(n)mim](+)-2Br(-)-1, and T4H(2)O-2[C(n)mim](+)-2Br(-)-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[C(n)mim](+)) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br-) is front > top. The stability order for the different microhydrates is following T-5H(2)O-1 < T-4H(2)O-Br--1 < T-3H(2)O-[C(n)mim](+)-Br--1 < T-2H(2)O-[C(n)mim](+)-2Br(-)-1 < T-H2O-2[C(n)mim](+)-2Br(-)-1. A good linear relationship between binding EB values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and pi-pi(+) stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [C(n)mim] cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr(-) complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and pi-pi cooperativity in the systems.

Automated summary

The mechanism of action of ionic liquids on nucleobase's structure and properties is still limited. This study investigates the binding model of the 1-alkyl-3-methylimidazolium bromide ionic liquids to thymine in water and microhydrated environments. The results show differences in stability and cooperativity of hydrogen bonding and pi-pi(+) stacking in the growing ionic clusters. This study provides important insights into the mechanism of action of ionic liquids.