Nucleic acid sample storage is of paramount importance in biotechnology and forensic sciences. Very recently, hydrated ionic liquids (ILs) have been identified as ideal media for long-term DNA storage. Hence, understanding the binding characteristics and molecular mechanism of interactions of ILs with DNA is of both practical and fundamental interest. Here, we employ molecular dynamics simulations and spectroscopic experiments to unravel the key factors that stabilize DNA in hydrated ILs. Both simulation and experimental results show that DNA maintains the native B-conformation in ILs. Simulation results further suggest that, apart from the electrostatic association of IL cations with the DNA backbone, groove binding of IL cations through hydrophobic and polar interactions contributes significantly to DNA stability. Circular dichroism spectral measurements and fluorescent dye displacement assay confirm the intrusion of IL molecules into the DNA minor groove. Very interestingly, the IL ions were seen to disrupt the water cage around DNA, including the spine of hydration in the minor groove. This partial dehydration by ILs likely prevents the hydrolytic reactions that denature DNA and helps stabilize DNA for the long term. The detailed understanding of IL-DNA interactions provided here could guide the future development of novel ILs, specific for nucleic acid solutes.

Using a 5 ns explicit atom molecular dynamics simulation of a 60 monomer sodium dodecyl sulfate micellar system containing 7579 TIP3P water molecules, the behavior of water in different electrostatic environments was examined. Structural evaluation of the system revealed that penetration of water molecules into the micelle was restricted to the headgroup region, leaving a 12 Å water-free hydrocarbon core. Water molecules near the headgroup exhibit a distortion of the water-water hydrogen bonding network due to headgroup oxygenwater hydrogen bond formation. The dynamic implications of this distortion are manifested in the decay of the dipole autocorrelation function, Φ(t) and translational diffusion coefficient. We observe that while the translational diffusion coefficient of water molecules in the first solvation shell of the micelle is reduced by less than a half of its value in bulk water, the slow component of the reorientational correlation function is slowed by one or two orders of magnitude.

Four molecular dynamics computer simulations have been performed to study the intrinsic width and the width due to thermal fluctuations of the water/carbon tetrachloride interface. We observed that thermal fluctuations have a capillary wave character. The surface tension calculated by using capillary wave formalism shows a very good agreement with the value obtained from the components of the pressure tensor.

The existence of microemulsions in the system composed of phosphate-based fluorosurfactant, water, and supercritical CO2 is demonstrated by small-angle neutron scattering experiments. A computer simulation study performed on a reverse micelle created in this system shows that the micelle remains stable over a 4 ns time period of the simulation. While the data obtained from the experiments provide information about the size of the reverse micelle, the data obtained from the simulations provide additional information about the shape and structure of such a micelle. Small-Angle Neutron Scattering Experiments The presence of microemulsion water pools was directly confirmed using SANS measurements on the KWS2 SANS facility 16 at the FRJ2 reactor in Jü lich, Germany, with a 48 × 48 cm 2 area detector with cell size 0.8 × 0.8 cm 2 and a wavelength

We performed a molecular dynamics simulation on a system containing a water pool inside the reverse micelle made up of an assembly of phosphate fluorosurfactant molecules dissolved in supercritical carbon dioxide. The water molecules in the first solvation shell of the headgroup lose the water to water tetrahedral hydrogen bonded network but are strongly bonded to the surfactant headgroups. This change in inter-water hydrogen bonding in connection with the confined geometry of the reverse micelle slows down the translational and especially the rotational dynamics of water.