In this article, we report a molecular dynamics simulation study on the X-ray and neutron scattering structures of deep eutectic solvents (DESs) and show that the DESs studied possess unique spatial heterogeneity on molecular length scales. The simulated X-ray and neutron scattering structure functions (S(q)s) of the DESs made of alkylamide + Li(+)/ClO4(-) display two peaks in the intermolecular region of the S(q)s. As a signature of nanoscale structural organization/heterogeneity, a prepeak is observed at 0.1 < q/Å(-1) < 0.4. The principal peak observed at around 1.2 < q/Å(-1) < 2 is rendered by short-distance inter- and intraspecies correlations. For the DESs studied, we demonstrate that nanoscale spatial heterogeneity is exhibited profoundly by the segregated domains of the constituent electrolyte, and the principal peak in S(q) is because of all sorts of close-contact correlations. The extent of nanoscale morphology as well as the strength of ion pairing is enhanced for the longer-tail alkylamide DES.

Recently, it has been observed that choline chloride ([Ch][Cl]) based deep eutectic solvents (DESs) may possess nanostructures in which chloride ions play a major role by providing a backbone for the bridged hydrogen bond network. In this article, we present a fundamental study on the role of hydration on the nanostructure of a [Ch][Cl] based DES, ethaline. In this molecular dynamics investigation, we observe a nonlinear change in the structural morphology of ethaline on gradual addition of water. The initiation of disruption of the native structure of the DES at 40 mol % of water is clearly observed, after which the increasing dilution rapidly destructs the long-range as well as short-range intermolecular interactions existing between the constituent species of pure ethaline. Herein, we find that, at very high hydration level, chloride ion no longer acts as a bridge between the choline cation and ethylene glycol, as it forms strong hydrogen bond with water. Intriguingly, the strengthening of hydrogen bonding interactions among the ethylene glycol molecules is observed on increasing hydration level. Hence, it is predicted that segregation of ethylene glycol can occur in the pool of aqueous mixtures of [Ch][Cl] at very high hydration level.

The structural landscape of room-temperature ionic liquids (RTILs) with longer cationic alkyl tail(s) exhibits polarity ordering (PO) along with charge ordering (CO). In polarity ordering, which is also referred to as intermediate-range ordering, polar groups are separated by segregated domains of apolar groups and vice versa. Charge ordering resembles alternation of positive-negative charge groups. In this work, how these two characteristic orderings respond to applied external pressure has been investigated via molecular dynamics simulations. The present study complements the recent experimental studies of Yoshimura et al. (J. Phys. Chem. B 2015, 119, 8146-8153) and computational studies of Russina et al. (Phys. Chem. Chem. Phys. 2015, 17, 29496-29500) wherein the authors described in detail the effects of pressure on the structural and conformational changes in imidazolium based ionic liquids. Our simulations predict that for 1-alkyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide, Pyrr1,n(+)/NTf2(-) with n = 8 and 10, the PO and CO fade when the external pressure increases from ambient pressure to 10000 bar. We observe that the apolar tail group as well as the polar group correlations are susceptible to the applied pressure. The decrease of polar-polar and apolar-apolar correlations at higher pressure is accompanied by the enhancement in the polar-apolar correlations and increased stability/probability of gauche conformations along the cationic tails.

We report here an all-atom energy based Monte Carlo docking procedure tested on a dataset of 226 protein-ligand complexes. Average root mean square deviation (RMSD) from crystal conformation was observed to be approximately 0.53 A. The correlation coefficient (r(2)) for the predicted binding free energies calculated using the docked structures against experimental binding affinities was 0.72. The docking protocol is web-enabled as a free software at www.scfbio-iitd.res.in/dock.

In the present molecular dynamics study, we investigate the effects of increasing pressure on the structural morphology of trihexyl(tetradecyl)phosphonium bromide (P/Br) and trihexyl(tetradecyl)phosphonium dicyanamide (P/DCA) ionic liquids (ILs). Special attention was paid to how charge and polarity orderings, which are present in the microscopic structure of these ILs at ambient conditions, respond to very high external pressure. The simulated X-ray scattering structure functions, S(q)s, of the two systems reveal that both the characteristic orderings show appreciable responsiveness towards the applied pressure change. At a given pressure, a slight difference between the polarity ordering (PO), charge ordering (CO), and adjacency correlations (AC) for both the systems points towards different microscopic structure of the two ILs due to change in anion. Beyond a certain pressure, we observe emergence of a new low-q peak in the S(q)s of both the systems. The new peak is associated with formation of crystalline order in these systems at higher pressures and the real space length-scale corresponding to the crystalline order lies in between those of polarity- and charge-ordering. Beyond the transition pressure, the crystallinity of both the systems increases with increasing pressure and the corresponding length-scale shifts towards smaller values upon increasing pressure. We also observe that the extent of the usual polarity ordering decreases upon increasing pressure for both the P/Br and P/DCA systems. We demonstrate that the disappearance of the usual polarity peak is due to decreased polar-polar and apolar-apolar correlations and enhanced correlations between the charged and uncharged groups of the ions. This scenario is completely reversed for the components corresponding to the crystalline order, the polar-polar and apolar-apolar correlations are enhanced and polar-apolar correlations are diminished at higher pressure. In addition, the charge ordering peak, which is not so obvious from the total S(q) but from ionic and sub-ionic partial components of it, shifts towards lower q values for P/Br. Instead, for the P/DCA, at the highest pressure studied the CO peak occurs at a q-value higher than that at the ambient pressure.