Solvation of Nucleobases in 1,3-Dialkylimidazolium Acetate Ionic Liquids: NMR Spectroscopy Insights into the Dissolution Mechanism

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.

Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations

We employed metadynamics-based classical molecular dynamics simulations to methylated adenine-thymine (mA-mT) and guanine-cytosine (mG-mC) base pairs to see favorable conformations in various concentrations of hydrated 1-ethyl, 3-methyl imidazolium acetate. We investigated various stacked and hydrogen-bonded conformations of association of base pairs through appropriately chosen collective variables. Stacked conformations more favored in water for both base pairs, whereas Watson-Crick (WC) hydrogen-bonding conformations are favored in pure and hydrated ionic liquids (ILs) except for 0.75 mol fraction IL. We observe that EMIm cations surround the base pairs in WC conformations creating a kind of hydrophobic cavity and protect the hydrogen bonds between base pairs. However, the five-membered heteroaromatic rings of cations stack with the nucleobases in the cation-base-cation (π-π-π) model, which resembles the base-base-base stacking in a DNA duplex. Interestingly, from additional simulations of 0.5 mol fraction hydrated choline dihydrogen phosphate IL, we observe that the stacked conformations become more favored than the WC conformation due to the absence of π-bonds in cations. The calculated values of relative solubility of base pairs in pure and hydrated ionic liquids compared to those in pure water correlate well with the free energy values of WC and stacked conformations.

Polyoxometalate catalysts for biomass dissolution: understanding and design

The use of polyoxometalate catalysts for selective delignification of biomass presents a possible route toward using ionic liquids (ILs) to efficiently obtain high-molecular weight biopolymers from biomass. Rapid progress in this area will depend on recognizing and using the link with already well-developed inorganic chemistry in ILs pursued outside the field of biomass processing. Here, we use crystal structures determined from single crystal X-ray diffraction to better understand the behavior of [PV2Mo10O40]5-, a polyoxometalate catalyst known for its ability to promote selective delignification of biomass in the IL 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]). The crystal structure of [C2mim]5[PV2Mo10O40]·THF shows the formation of cationic shells around the anions which are likely representative of the interactions of this catalyst with [C2mim][OAc] itself. The reaction of NH4VO3 with [C2mim][OAc] is explored to better understand the chemistry of vanadium(V), which is critical to redox catalysis of [PV2Mo10O40]5-. This reaction gives crystals of [C2mim]4[V4O12], showing that this IL forms discrete metavanadates which are obtained from aqueous solutions in a specific pH range and indicating that the basicity of [OAc]- dominates the speciation of vanadium (V) in this IL.

Biosolvation Nature of Ionic Liquids: Molecular Dynamics Simulation of Methylated Nucleobases in Hydrated 1-Ethyl-3-methylimidazolium Acetate

Solvation free energies of methylated nucleobases were calculated in pure and hydrated 1-ethyl-3-methylimidazolium acetate, [Emim][Ac], ionic liquid, and pure water using classical molecular dynamics simulations using multistate Bennett's acceptance ratio method. The calculated solvation free energies in pure water were compared with the previous experimental and theoretical findings and found to be in agreement. We observe that the solvation free energy of methylated nucleobases is more in the pure ionic liquid compared to that in the pure water and on changing the mole fraction of water in the ionic liquid, the solvation free energy decreases gradually. Comparing the Coulombic and van der Waals contribution to the solvation free energy, electrostatic contribution is more compared to that of the latter for all nucleobases. To obtain the atomistic details and explain the solvation mechanism, we calculated radial distribution functions (RDFs), spatial distribution functions (SDFs), and stacking angle distribution of cations to the nucleobases. From RDFs and SDFs, we find that the acetate anions of the ionic liquid are forming strong hydrogen bonds with the amine hydrogen atoms of the nucleobases. These hydrogen bonds contribute to the major part of the Coulombic contribution to the solvation free energy. Stacking of cations to the nucleobases is primarily due to the van der Waals contribution to the solvation free energy.

Design of task-specific fluorinated ionic liquids: nanosegregation versus hydrogen-bonding ability in aqueous solutions

Fluorinated ionic liquids rich-nanosegregated behaviour reduces the impact of the addition of water upon the ionic liquids's H-bond acceptance ability.

Formation of ionic co-crystals of amphoteric azoles directed by the ionic liquid co-former 1-ethyl-3-methylimidazolium acetate

The ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate was utilized as a liquid-state crystallization agent to form ionic co-crystals using amphoteric azoles selected as model compounds for active pharmaceutical ingredients. Weakly acidic azoles crystallize the IL relatively quickly, while stronger acidic azoles undergo slower ion exchange with the IL to form salts.

Solvation Structure of Uracil in Ionic Liquids

The local solvation environment of uracil dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute (ionic liquid:uracil) ratios of 3:1 and 2:1, little perturbation of the ion-ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia-Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109-4120). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favourable uracil-uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution.

New Insights into CO2 Absorption Mechanisms with Amino-Acid Ionic Liquids

The last decade saw an explosion of interest in using amine-functionalized materials for CO2 capture and conversion, and it is of great importance to elucidate the relationship between the molecular structure of amine-functionalized materials and their CO2 capacity. In this work, based on a new quantitative analysis method for the CO2 absorption mechanism of amino-acid ionic liquids (ILs) and quantum chemical calculations, we show that the small difference in the local structure of amine groups in ILs could lead to much different CO2 absorption mechanisms, which provides an opportunity for achieving higher CO2 capacity by structure design. This work revealed that the actual CO2 absorption mechanism by amino-acid ILs goes beyond the apparent CO2 /amine stoichiometry; a rigid ring structure around the amine group in ILs creates a unique electrostatic environment that inhibits the deprotonation of carbamic acid and enables actually equimolar CO2 /amine absorption.

Ion-water wires in imidazolium-based ionic liquid/water solutions induce unique trends in density

Ionic liquid/water binary mixtures are rapidly gaining popularity as solvents for dissolution of cellulose, nucleobases, and other poorly water-soluble biomolecules. Hence, several studies have focused on measuring the thermophysical properties of these versatile mixtures. Among these, 1-ethyl-3-methylimidazolium ([emim]) cation-based ILs containing different anions exhibit unique density behaviours upon addition of water. While [emim][acetate]/water binary mixtures display an unusual rise in density with the addition of low-to-moderate amounts of water, those containing the [trifluoroacetate] ([Tfa]) anion display a sluggish decrease in density. The density of [emim][tetrafluoroborate] ([emim][BF4])/water mixtures, on the other hand, declines rapidly in close accordance with the experimental reports. Here, we unravel the structural basis underlying this unique density behavior of [emim]-based IL/water mixtures using all-atom molecular dynamics (MD) simulations. The results revealed that the distinct nature of anion-water hydrogen bonded networks in the three systems was a key in modulating the observed unique density behaviour. Vast expanses of uninterrupted anion-water-anion H-bonded stretches, denoted here as anion-water wires, induced significant structuring in [emim][Ac]/water mixtures that resulted in the density rise. Conversely, the presence of intermittent large water clusters disintegrated the anion-water wires in [emim][Tfa]/water and [emim][BF4]/water mixtures to cause a monotonic density decrease. The differential nanostructuring affected the dynamics of the solutions proportionately, with the H-bond making and breaking dynamics found to be greatly retarded in [emim][Ac]/water mixtures, while it exhibited a faster relaxation in the other two binary solutions.

High Nucleobase-Solubilizing Ability of Low-Viscous Ionic Liquid/Water Mixtures: Measurements and Mechanism

Research on nucleobases has always been on the forefront owing to their ever-increasing demand in the pharmaceutical, agricultural, and other industries. The applications, however, became limited due to their poor solubility in water. Recently, ionic liquids (ILs) have emerged as promising solvents for nucleobase dissolution, as they exhibit >100-fold increased solubility compared to water. But the high viscosity of ILs remains as a bottleneck in the field. Here, by solubility and viscosity measurements, we show that addition of low-to-moderate quantity of water preserves the high solubilizing capacity of ILs, while reducing the viscosity of the solution by several folds. To understand the mechanism of nucleobase dissolution, molecular dynamics simulations were carried out, which showed that at low concentrations water incorporates into the IL-nucleobase network without much perturbing of the nucleobase-IL interactions. At higher concentrations, increasing numbers of IL anion-water hydrogen bonds replace IL-nucleobase interactions, which have been confirmed by (1)H- and (13)C NMR chemical shifts of the IL ions.

Cholinium-based ionic liquids with pharmaceutically active anions

Ionic liquids with cholinium-based active pharmaceutical ingredients (API-ILs) were preparedviaa simple and sustainable two-step anion exchange reaction. The resulting salts have improved upon the chemical, physical and biopharmaceutical properties of the parent APIs.

Quantitative evaluation of myoglobin unfolding in the presence of guanidinium hydrochloride and ionic liquids in solution

The use of ionic liquids in biochemical and biophysical applications has increased dramatically in recent years due to their interesting properties. We report results of a thermodynamic characterization of the chaotrope-induced denaturation of equine myoglobin in two different ionic liquid aqueous environments using a combined absorption/fluorescence spectroscopic approach. Denaturation by guanidinium hydrochloride was monitored by loss of heme absorptivity and limited unfolding structural information was obtained from Förster resonance energy transfer experiments. Results show that myoglobin unfolding is generally unchanged in the presence of ethylmethylimidazolium acetate (EMIAc) in aqueous solution up to 150 mM concentration but is facilitated by butylmethylimidazolium boron tetrafluoride (BMIBF4) in solution. The presence of 150 mM BMIBF4 alone does not induce unfolding but destabilizes the structure as observed by a decrease in threshold denaturant concentration for unfolding and an 80% decrease in the magnitude of ΔGunfolding from 44 kJ/mol in the absence of BMIBF4 to 8 kJ/mol in the presence of 150 mM BMIBF4. Thus, the BMIBF4 significantly destabilizes the myoglobin structure while the EMIAc does not, likely due to differences in anion interaction capabilities. This is confirmed with control studies using NaAc and LiBF4 solutions. EMIAc may be chosen as cosolvent additive with minimal effects on protein structure while BMIBF4 may be used as a supplement in protein folding experiments, potentially allowing access to proteins which have been traditionally difficult to denature as well as designing ionic liquids to match protein characteristics.