Effect of a molecule of imidazolium bromide ionic liquid on the structure and properties of cytosine by density functional theory

Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmim]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 ([Cnmim]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 + wH2O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH2O-y[Cnmim]+-xBr−, w = 5~1 and x + y = 0~4) 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-4H2O-Br−-1, T-3H2O-[Cnmim]+-Br−-1, T-2H2O-[Cnmim]+-2Br−-1, and T-1H2O-2[Cnmim]+-2Br−-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[Cnmim]+) 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-5H2O-1 < T-4H2O-Br−-1 < T-3H2O-[Cnmim]+-Br−-1 < T-2H2O-[Cnmim]+-2Br−-1 < T-1H2O-2[Cnmim]+-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 π-π+ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [Cnmim]+ 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 π-π cooperativity in the systems.

A Systematic Study of DFT Performance for Geometry Optimizations of Ionic Liquid Clusters

Clusters of two ion pairs of imidazolium-based ionic liquids were optimized with 43 different levels of theory, including DFT functionals and MP2-based methods combined with varying Dunning's basis sets, and added dispersion corrections. Better preforming DFT functionals were then applied to clusters consisting of four ion pairs. Excellent performance of some DFT functionals for the two ion pair clusters did not always match that of the four ion-paired clusters despite interionic distances remaining constant between the optimized two and four ion-paired clusters of the same ionic liquid. Combinations of DFT functional and basis set such as ωB97X-D/cc-pVDZ, M06-2X/aug-cc-pVDZ, B3LYP-D3/cc-pVTZ, and TPSS-D3/cc-pVTZ gave excellent results for geometry optimization of two ion-paired clusters of imidazolium ionic liquids but gave larger deviations when applied to the four ion-paired clusters of varying ionic liquids. Empirical dispersion corrections were seen to be crucial in correctly capturing correlation effects in the studied ionic liquid clusters, becoming more important in larger clusters. Dunning's double-ζ basis set, cc-pVDZ, is associated with the smallest root mean squared deviations for geometries; however, it also produces the largest deviations in total electronic energies. ωB97X-D and M06-2X produced the best performance with the augmented version of this basis set. The triple-ζ basis set, cc-pVTZ, leads to the best performance of most of the DFT functionals (especially the dispersion-corrected ones) used, whereas its augmented version, aug-cc-pVTZ, was not seen to improve results. The combinations of functional and basis set that gave the best geometry and energetics in both two and four ion-paired clusters were PBE-D3/cc-pVTZ, ωB97X-D/aug-cc-pVDZ, and BLYP-D3/cc-pVTZ. All three combinations are recommended for geometry optimizations of larger clusters of ionic liquids. PBE-D3/cc-pVTZ performed the best with an average deviation of 2.3 kJ mol^-1 and a standard deviation of 3.4 kJ mol^-1 for total electronic energy when applied to four ion-paired clusters. Geometries optimized with FMO2-SRS-MP2/cc-pVTZ produced total energy within 2.0 kJ mol^-1 off the benchmark in two ion-paired clusters, with the cc-pVDZ basis set performing unsurprisingly poorly with the same method. The error increased to 4.8 kJ mol^-1 on average in four ion-paired clusters, with the smallest RMSD deviations in geometries when compared to the benchmark ones. This study is the first report that investigated the performance of DFT functionals for two and four ion-paired clusters of a wide range of ionic liquids consisting of commonly used cations such as pyrrolidinium, imidazolium, pyridinium, and ammonium. It also identified the importance of assessing the performance of quantum chemical methods for ionic liquids on a variety of cation-anion combinations.

Impact of alkyl chain length and water on the structure and properties of 1-alkyl-3-methylimidazolium chloride ionic liquids

Conformational isomerism in C_nmim Cl (n = 2, 4, 6, 8, and 10) is identified by marker IR bands for the first time.

Pressure-Dependent Stability of Imidazolium-Based Ionic Liquid/DNA Materials Investigated by High-Pressure Infrared Spectroscopy

1-Butyl-3-methylimidazolium hexafluorophosphate ([C₄MIM][PF₆])/DNA and 1-methyl-3-propylimidazolium hexafluorophosphate ([C₃MIM][PF₆])/DNA mixtures were prepared and characterized by high-pressure infrared spectroscopy. Under ambient pressure, the imidazolium C²-H and C^4,5-H absorption bands of [C₄MIM][PF₆]/DNA mixture were red-shifted in comparison with those of pure [C₄MIM][PF₆]. This indicates that the C²-H and C^4,5-H groups may have certain interactions with DNA that assist in the formation of the ionic liquid/DNA association. With the increase of pressure from ambient to 2.5 GPa, the C²-H and C^4,5-H absorption bands of pure [C₄MIM][PF₆] displayed significant blue shifts. On the other hand, the imidazolium C-H absorption bands of [C₄MIM][PF₆]/DNA showed smaller frequency shift upon compression. This indicates that the associated [C₄MIM][PF₆]/DNA conformation may be stable under pressures up to 2.5 GPa. Under ambient pressure, the imidazolium C²-H and C^4,5-H absorption bands of [C₃MIM][PF₆]/DNA mixture displayed negligible shifts in frequency compared with those of pure [C₃MIM][PF₆]. The pressure-dependent spectra of [C₃MIM][PF₆]/DNA mixture revealed spectral features similar to those of pure [C₃MIM][PF₆]. Our results indicate that the associated structures of [C₄MIM][PF₆]/DNA are more stable than those of [C₃MIM][PF₆]/DNA under high pressures.