Local Structure Of Water Molecules Research Articles

Water molecule ordering on the surface of an intrinsically disordered protein

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.

Molecular insights into the heterogeneous crystal growth of tetrahydrofuran hydrate: Kinetic and interfacial properties

The present work aimed to explore molecular insight into the tetrahydrofuran (THF) hydrate growth along its crystallographic face to consider the heterogeneous conditions. Molecular dynamic (MD) simulation results provided detailed dynamical aspects of water, and THF molecules at the interface of aqueous solution/hydrate slab by using the F3 order parameter, and visual snapshots of the system at different times. Our simulations revealed that the interfacial properties of the hydrate phase can change the local structure of water molecules in the liquid phase and thus alter the kinetics of hydrate formation. Furthermore, the behavior of THF solution on the copper surface under the hydrate-forming conditions has been studied. It was found that the copper surface affected the THF solution by changing the distribution of THF and water molecules near the liquid-solid interface. Also, the MD simulation showed that a layer of THF molecules was adsorbed on the copper surface and subsequently, a dense water film was formed resulting in a strong resistance to order the water molecules around the THF for hydrate formation. These results are illustrative of how interfacial properties can affect the heterogeneous crystal growth of the hydrate phase.

Effects of interfaces on structure and dynamics of water droplets on a graphene surface: A molecular dynamics study

The structure and dynamics of water droplets on a bilayer graphene surface are investigated using molecular dynamics simulations. The effects of solid/water and air/water interfaces on the local structure of water droplets are analyzed in terms of the hydrogen bond distribution and tetrahedral order parameter. It is found that the local structure in the core region of a water droplet is similar to that in liquid water. On the other hand, the local structure of water molecules at the solid/water and air/water interfaces, referred to as the interface and surface regions, respectively, consists mainly of three-coordinated molecules that are greatly distorted from a tetrahedral structure. This study reveals that the dynamics in different regions of the water droplets affects the intermolecular vibrational density of states: It is found that in the surface and interface regions, the intensity of vibrational density of states at ∼50 cm-1 is enhanced, whereas those at ∼200 and ∼500 cm-1 are weakened and redshifted. These changes are attributed to the increase in the number of molecules having fewer hydrogen bonds in the interface and surface regions. Both single-molecule and collective orientation relaxations are also examined. Single-molecule orientation relaxation is found to be marginally slower than that in liquid water. On the other hand, the collective orientation relaxation of water droplets is found to be significantly faster than that of liquid water because of the destructive correlation of dipole moments in the droplets. The negative correlation between distinct dipole moments also yields a blueshifted libration peak in the absorption spectrum. It is also found that the water-graphene interaction affects the structure and dynamics of the water droplets, such as the local water structure, collective orientation relaxation, and the correlation between dipole moments. This study reveals that the water/solid and water/air interfaces strongly affect the structure and intermolecular dynamics of water droplets and suggests that the intermolecular dynamics, such as energy relaxation dynamics, in other systems with interfaces are different from those in liquid water.

Characterization of water structure in carbon nanotubes by various order parameters

Various order parameters have been suggested to characterize the local structure of liquid water in bulk. Characterization the local structure of water molecules in the confined systems by various order parameters is important but still unclear. In this work, a series of popular order parameters are used to analyze the local structure of water molecules in carbon nanotubes (CNTs) by molecular dynamics simulation. Based on the value of order parameters, the different structures of water molecules in CNTs and in bulk were discussed. The orientational tetrahedral order (q) and translational tetrahedral order (Sk) are much better than local structure index (LSI) to describe the local structure of water in CNTs. We also demonstrated that the local structure of water molecules in the CNT(40,40) is almost the same with that in bulk. The findings could give us a guideline to investigate the water molecules in confined system.

Confirmation of local water structure confined in ionic liquids using H/D exchange

We investigated the local structure of water molecules confined inside ionic liquid (IL) nanodomain structures of 1-butyl-3-methylimidazolium tetrafluoroborate, (abbreviated as [bmim][BF4]) using NMR and Raman spectroscopy to monitor H/D exchange reaction between H2O and D2O water molecules. The results showed that fewer than 5 water molecules were probably present in the water domain of the IL nanospace at less than ~60 water mol%, where the translational motion of water molecules was inhibited and proton exchange rate was highly restricted. These phenomena were attributed to the absence of bulk hydrogen-bonded network structures in the water domain. The H atoms of the HDO molecule tended to interact with BF4− anions, whereas the D atoms of HDO interacted with the C2 atoms of the bmim+ cation. As a result, water molecules became trapped inside the IL framework, which is likely to be the main cause of the reduction in H/D exchange rate among water molecules in the mixture.

Further Insight into the Definite Morphology and Formation Mechanism of Mesoporous Silica KCC-1.

The unique three-dimensional pore structure of KCC-1 has attracted significant attention and has proven to be different compared to other conventional mesoporous silica such as the MCM-41 family, SBA-15, or even MSN nanoparticles. In this research, we carefully examine the morphology of KCC-1 to define more appropriate nomenclature. We also propose a formation mechanism of KCC-1 based on our experimental evidence. Herein, the KCC-1 morphology was interpreted mainly on the basis of compiling all observation and information taken from SEM and TEM images. Further analysis on TEM images was carried out. The gray value intensity profile was derived from TEM images in order to determine the specific pattern of this unique morphology that is found to be clearly different from that of other types of porous spherical-like morphologies. On the basis of these results, the KCC-1 morphology would be more appropriately reclassified as bicontinuous concentric lamellar morphology. Some physical characteristics such as the origin of emulsion, electrical conductivity, and the local structure of water molecules in the KCC-1 emulsion were disclosed to reveal the formation mechanism of KCC-1. The origin of the KCC-1 emulsion was characterized by the observation of the Tyndall effect, conductometry to determine the critical micelle concentration, and Raman spectroscopy. In addition, the morphological evolution study during KCC-1 synthesis completes the portrait of the formation of mesoporous silica KCC-1.

How Properties of Solid Surfaces Modulate the Nucleation of Gas Hydrate.

Molecular dynamics simulations were performed for CO2 dissolved in water near silica surfaces to investigate how the hydrophilicity and crystallinity of solid surfaces modulate the local structure of adjacent molecules and the nucleation of CO2 hydrates. Our simulations reveal that the hydrophilicity of solid surfaces can change the local structure of water molecules and gas distribution near liquid-solid interfaces, and thus alter the mechanism and dynamics of gas hydrate nucleation. Interestingly, we find that hydrate nucleation tends to occur more easily on relatively less hydrophilic surfaces. Different from surface hydrophilicity, surface crystallinity shows a weak effect on the local structure of adjacent water molecules and on gas hydrate nucleation. At the initial stage of gas hydrate growth, however, the structuring of molecules induced by crystalline surfaces are more ordered than that induced by amorphous solid surfaces.

Static and dynamic heterogeneities in water

The thermodynamic behaviour of water seems to be related to static heterogeneities. These static heterogeneities are related to the local structure of water molecules and, when properly characterized, may offer an economical explanation of thermodynamic data. 'What matters' most in determining some of the unusual properties of liquid water may be the fact that the local geometry of the liquid molecules is not spherical or oblong, but rather tetrahedral. In respect to static heterogeneities, this local geometry is critical. The dynamic behaviour of water seems to be related to dynamic heterogeneities, which seem to explain the dynamics of supercooled liquid water well.

Static heterogeneities in liquid water

The thermodynamic behavior of water seems to be closely related to static heterogeneities. These static heterogeneities are related to the local structure of water molecules, and when properly characterized, may offer an economical explanation of thermodynamic data. The key feature of liquid water is not so much that the existence of hydrogen bonds, first pointed out by Linus Pauling, but rather the local geometry of the liquid molecules is not spherical or oblong but tetrahedral. In the consideration of static heterogeneities, this local geometry is critical. Recent experiments suggested more than one phase of amorphous solid water, while simulations suggest that one of these phases is metastable with respect to another, so that in fact there are only two stable phases.

Light metal ions in water: Quantal and classical simulations for 7Li+

Path integral Monte Carlo computations have been done to study the local structure of water molecules around an isolated lithium ion ( 7Li +) at T=298K. The solute was treated as a quantal particle and the water solvent was treated classically. The water-water interaction was modelled by the MCY pair-potential and the solute-water interaction by the Kistenmacher et al. pair-potential. Purely classical simulations, at the same conditions and using the same model potentials, where also performed for comparison. Significant changes are observed on the results of the quantal simulations when compared with the results of the classical simulation. The major difference is the coordination number that increases from 5, the result of the classical simulation, to 6, for the quantal simulation. In addition, structural analysis of the generated configurations showed that the local structure of the water molecules surrounding the ion is also clearly different in the two simulations. The reliability of the results is discussed.