No abstract

Atomistic simulations have been performed to investigate the effect of aliphatic chain length in tetraalkylphosphonium cations on liquid morphologies, microscopic ionic structures, and dynamical quantities of tetraalkylphosphonium chloride ionic liquids. The liquid morphologies are characterized by sponge-like interpenetrating polar and apolar networks in ionic liquids consisting of tetraalkylphosphonium cations with short aliphatic chains. The lengthening aliphatic chains in tetraalkylphosphonium cations lead to polar domains consisting of chloride anions and central polar groups in cations being partially or totally segregated in ionic liquid matrices due to a progressive expansion of apolar domains in between. Prominent polarity alternation peaks and adjacency correlation peaks are observed at low and high q range in total X-ray scattering structural functions, respectively, and their peak positions gradually shift to lower q values with lengthening aliphatic chains in tetraalkylphosphonium cations. The charge alternation peaks registered in the intermediate q range exhibit complicated tendencies due to a cancellation of peaks and anti-peaks in partial structural functions for ionic subcomponents. The particular microstructures and liquid morphologies in tetraalkylphosphonium chloride ionic liquids intrinsically contribute to distinct dynamics characterized by mean square displacements, van Hove correlation functions, and non-Gaussian parameters for ionic species in the heterogeneous ionic environment. Most tetraalkylphosphonium cations have higher translational mobilities than their partner anions due to strong coordination of chloride anions with central polar groups in tetraalkylphosphonium cations through strong Coulombic and hydrogen bonding interactions. The increase of aliphatic chain length in tetraalkylphosphonium cations leads to a concomitant shift of van Hove correlation functions and non-Gaussian parameters to larger radial distances and longer time scales, respectively, indicating the enhanced translational dynamical heterogeneities of tetraalkylphosphonium cations and the corresponding chloride anions.

Intermolecular features like hydrogen bonding and π-type interactions play pivotal roles in stabilizing molecular structures in ionic liquids with planar rings and hydrogen-bond donors and acceptors. However, the delicate interplay among these interactions is complicated and depends on specific ion types. In this work, ab initio molecular dynamics simulations were performed to reveal competitive and cooperative characteristics among hydrogen bonding and π-type interactions in a typical imidazolium-oxalatoborate ionic liquid. Imidazolium rings take preferential on-top parallel orientations, leading to their particular π-π stacking distributions at short distances. Intermolecular interactions between imidazolium and oxalato rings are manifested by short-range on-top parallel orientations and in-plane hydrogen bonding interactions, promoting their parallel displaced offset stacking arrangements. However, on an intermediate distance scale, attractive Coulombic interactions between imidazolium and oxalato rings dominate and contribute to their perpendicular orientations. Spatial coordination patterns between intermolecular oxalato rings are balanced by repulsive electrostatic interactions and steric hindrance effects, leading to their tilted orientations in local environments.

Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K(+) ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K(+) as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew model are found to be closest to the experimental data at all of the studied ion concentrations.