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G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although extensively studied through various experimental and computational methods, hydration patterns near DNA remain under debate due to the chemically and topologically heterogeneous nature of the exposed surface. In this work, we employed all-atom molecular dynamics (MD) simulation to study the hydration patterns of GQ DNA. The Drude oscillator model was used in MD simulation as a computationally efficient method for modeling electronic polarization in DNA ion solutions. Hydration structure was analyzed in terms of radial distribution functions and high-density three-dimensional hydration sites. Analysis of hydration dynamics focused on self-diffusion rates and orientation time correlation at different structural regions of GQ DNA. The results show highly heterogeneous hydration patterns in both structure and dynamics; for example, there are several insular high-density sites in the inner channel, and ‘spine of water’ in the groove. For water inside the loop, anomalous diffusion is present over a long time scale, but for water around the phosphate group and groove, diffusion becomes normal after ∼ 30 ps. These essentially correspond to deeply buried structural water and strong interaction with DNA, respectively.

G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics (MD), and steered MD (SMD) simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions (K+/Na+) is about the base stacking free energies indicates that there will be a competition among the binding of M+-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+ was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.

We theoretically and experimentally show that, with water being adsorbed, the graphene oxide (GO) is converted to a spontaneously dynamic covalent material under ambient conditions, where the dominated epoxy and hydroxyl groups are mediated by water molecules to spontaneously break/reform their C–O bonds to achieve dynamic oxygen migration. This dynamic material presents structural adaptivity for response to biomolecule adsorption. Both density functional theory calculations and ab initio molecular dynamics simulations demonstrate that this spontaneously dynamic characteristics is attributed to the adsorption of water molecules, which sharply reduces the barriers of these oxygen migration reactions on GO to the level less than or comparable to the hydrogen bonding energy in liquid water.

Single-file transportation of water across narrow nanochannels such as carbon nanotubes has attracted much attention in recent years. Such permeation can be greatly affected by the water-channel interactions; despite some progress, this issue has not been fully explored. Herein we use molecular dynamics simulations to investigate the effects of water-channel attractions on occupancy, translational (transportation) and orientational dynamics of water inside narrow single-walled carbon nanotubes (SWNTs). We use SWNTs as the model nanochannels and change the strength of water-nanotube attractions to mimic the changes in the hydrophobicity/polarity of the nanochannel. We investigate the dependence of water occupancy inside SWNTs on the water-channel attraction and identify the corresponding threshold values for drying states, wetting-drying transition states, and stably wetting states. As the strength of water-channel attractions increases, water flow increases rapidly first, and then decreases gradually; the maximal flow occurs in the case where the nanochannel is predominately filled with the 1D water wire but with a small fraction of 'empty states', indicating that appropriate empty-filling (drying-wetting) switching can promote water permeation. This maximal flow is unexpected, since in traditional view, the stable and tight hydrogen-bonding network of the water wire is the prerequisite for high permeability of water. The underlying mechanism is discussed from an energetic perspective. In addition, the effect of water-channel attractions on reorientational dynamics of the water wire is studied, and a negative correlation between the flipping frequency of water wire and the water-channel attraction is observed. The underlying mechanism is interpreted in term of the axial total dipole moment of inner water molecules. This work would help to better understand the effects of water-channel attractions on wetting properties of narrow nanochannels, and on single-file water permeation through nanochannels, which might be helpful in designs of high-flux nanochannels.

How to determine accurately the association states of solutes in aqueous systems is of fundamental importance in a variety of chemical, physical, and biological processes. We apply four widely used criteria to analyze the dynamic association processes of solutes, e.g., amphiphilic molecules, and to find the inappropriate selections of representative sites on solutes in these criteria may bring about appreciable influence on the estimation of dynamic association behaviors such as unrealistic packing radii and even misleading packing structures. It would be better to select dynamically representative sites on solute molecules based on the characteristic of solute associations. Our detailed discussions give a guide on how to determine an appropriate criterion to accurately analyze the association behaviors of solute molecules in aqueous solutions.

Using a primitive water model, we find that the strength of tetrahedral interactions can change the behavior of liquid water from the liquid-liquid critical point scenario to the singularity-free scenario. Specifically, we find that the strongly tetrahedral model has a liquid-liquid critical point from which the Widom line emanates with a negative slope, but that the weakly tetrahedral model lacks the second critical point and the line of the specific heat maxima analogous to the Widom line has a positive slope. The strongly tetrahedral interaction is characterized by a double-step potential that depends on hydrogen-bond bending, while the weakly tetrahedral interaction has a uniform single-step potential.