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Register a new userNetwork Topology in Water Nanoconfined between Phospholipid Membranes
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Water provides the driving force for the assembly and stability of many cellular components. Despite its impact on biological functions, a nanoscale understanding of the relationship between its structure and dynamics under soft confinement has remained elusive. As expected, water in contact with biological membranes recovers its bulk density and dynamics at $sim 1$ nm from phospholipid headgroups but surprisingly enhances its intermediate-range order (IRO) over a distance, at least, twice as large. Here, we explore how the IRO is related to the waters hydrogen bond network (HBN) and its coordination defects. We characterize the increased IRO by an alteration of the HBN up to more than eight coordination shells of hydration water. The HBN analysis emphasizes the existence of a bound-unbound water interface at $sim 0.8$ nm from the membrane. The unbound water has a distribution of defects intermediate between bound and bulk water, but with density and dynamics similar to bulk, while bound water has reduced thermal energy and much more HBN defects than low-temperature water. This observation could be fundamental for developing nanoscale models of biological interactions and for understanding how alteration of the water structure and topology, for example, due to changes in extracellular ions concentration, could affect diseases and signaling. More generally, it gives us a different perspective to study nanoconfined water.
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An accurate description of the structure and dynamics of interfacial water is essential for phospholipid membranes, since it determines their function and their interaction with other molecules. Here we consider water confined in stacked membranes with hydration from poor to complete, as observed in a number of biological systems. Experiments show that the dynamics of water slows down dramatically when the hydration level is reduced. All-atom molecular dynamics simulations identify three (inner, hydration and outer) regions, within a distance of approximately 1 nm from the membrane, where water molecules exhibit different degrees of slowing down in the dynamics. The slow-down is a consequence of the robustness of the hydrogen bonds between water and lipids and the long lifetime of the hydrogen bonds between water molecules near the membrane. The interaction with the interface, therefore, induces a structural change in the water that can be emphasized by calculating its intermediate range order. Surprisingly, at distances as far as ~ 2.5 nm from the interface, although the bulk-like dynamics is recovered, the intermediate range order of water is still slightly higher than that in the bulk at the same thermodynamic conditions. Therefore, the water-membrane interface has a structural effect at ambient conditions that propagates further than the often-invoked 1 nm length scale. Membrane fluctuations smear out this effect macroscopically, but an analysis performed by considering local distances and instantaneous configurations is able to reveal it, possibly contributing to our understanding of the role of water at biomembrane interfaces.
Free volume pockets or voids are important to many biological processes in cell membranes. Free volume fluctuations are a prerequisite for diffusion of lipids and other macromolecules in lipid bilayers. Permeation of small solutes across a membrane, as well as diffusion of solutes in the membrane interior are further examples of phenomena where voids and their properties play a central role. Cholesterol has been suggested to change the structure and function of membranes by altering their free volume properties. We study the effect of cholesterol on the properties of voids in dipalmitoylphosphatidylcholine (DPPC) bilayers by means of atomistic molecular dynamics simulations. We find that an increasing cholesterol concentration reduces the total amount of free volume in a bilayer. The effect of cholesterol on individual voids is most prominent in the region where the steroid ring structures of cholesterol molecules are located. Here a growing cholesterol content reduces the number of voids, completely removing voids of the size of a cholesterol molecule. The voids also become more elongated. The broad orientational distribution of voids observed in pure DPPC is, with a 30% molar concentration of cholesterol, replaced by a distribution where orientation along the bilayer normal is favored. Our results suggest that instead of being uniformly distributed to the whole bilayer, these effects are localized to the close vicinity of cholesterol molecules.
Nanoconfinement can drastically change the behavior of liquids, puzzling us with counterintuitive properties. Moreover, it is relevant in applications, including decontamination and crystallization control. It still lacks a systematic analysis for fluids with different bulk properties. Here we fill this gap. We compare, by molecular dynamics simulations, three different liquids in a graphene slit pore: (A) A simple fluid, such as argon, described by a Lennard-Jones potential; (B) An anomalous fluid, such as a liquid metal, modeled with an isotropic core-softened potential; (C) Water, the prototypical anomalous liquid, with directional hydrogen bonds. We study how the slit-pore width affects the structure, thermodynamics, and dynamics of the fluids. We check that all the fluids, as expected, show similar oscillating properties by changing the pore size. However, the nature of the free-energy minima for the three fluids is quite different: i) only for the simple liquid all the minima are energy-driven, while their structural order increases with decreasing slit-pore width; ii) only for the isotropic core-softened potential all the minima are entropy-driven, while the energy in the minima increases with decreasing slit-pore width; iii) only the water has a changing nature of the minima: the monolayer minimum is entropy-driven, at variance with the simple liquid, while the bilayer minimum is energy-driven, at variance with the other anomalous liquid. Also, water diffusion has a large increase for sub-nm slit-pores, becoming faster than bulk. Instead, the other two fluids have diffusion oscillations much smaller than water slowing down for decreasing slit-pore width. Our results clarify that nanoconfined water is unique compared to other (simple or anomalous) fluids under similar confinement, and are possibly relevant in nanopores applications, e.g., in water purification from contaminants.
We report a high energy-resolution neutron backscattering study, combined with in-situ diffraction, to investigate slow molecular motions on nanosecond time scales in the fluid phase of phospholipid bilayers of 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine (DMPC) and DMPC/40% cholesterol (wt/wt). A cooperative structural relaxation process was observed. From the in-plane scattering vector dependence of the relaxation rates in hydrogenated and deuterated samples, combined with results from a 0.1 microsecond long all atom molecular dynamics simulation, it is concluded that correlated dynamics in lipid membranes occurs over several lipid distances, spanning a time interval from pico- to nanoseconds.
Over the years, plenty of classical interaction potentials for water have been developed and tested against structural, dynamical and thermodynamic properties. On the other hands, it has been recently observed (F. Martelli et. al, textit{ACS Nano}, textbf{14}, 8616--8623, 2020) that the topology of the hydrogen bond network (HBN) is a very sensitive measure that should be considered when developing new interaction potentials. Here we report a thorough comparison of 11 popular non polarizable classical water models against their HBN, which is at the root of water properties. We probe the topology of the HBN using the ring statistics and we evaluate the quality of the network inspecting the percentage of broken and intact HBs. For each water model, we assess the tendency to develop hexagonal rings (that promote crystallization at low temperatures) and pentagonal rings (known to frustrate against crystallization at low temperatures). We then introduce the emph{network complexity index}, a general descriptor to quantify how much the topology of a given network deviates from that of the ground state, namely of hexagonal or cubic ice. Remarkably, we find that the network complexity index allows us to relate, for the first time, the dynamical properties of different water models with their underlying topology of the HBN. Our study provides a benchmark against which the performances of new models should be tested against, and introduces a general way to quantify the complexity of a network which can be transferred to other materials and that links the topology of the HBN with dynamical properties. Finally, our study introduces a new perspective that can help in rationalizing the transformations among the different phases of water and of other materials.
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