Dynamic Behavior Of Water Molecules Research Articles

The influence of force fields on the structure and dynamics of water confined in ZIF-8 from atomistic simulations.

The complexity of modeling flexible crystals, such as ZIF-8, mainly stems from the handling of intramolecular interactions. Numerous force fields have been proposed in the literature to describe the interactions between atoms in ZIF-8. We employ seven force fields to examine the structure and dynamic behavior of water molecules confined in ZIF-8, with the aim of investigating the impact of force fields on simulation results. Various structural characterization methods consistently indicate that the choice of different force fields has quantitative effects but no qualitative effects on the structural characteristics of confined water. Additionally, the force fields do not impact the qualitative description of the diffusion mechanism. Both mean-square displacement and van Hove autocorrelation function reveal two characteristic movements of water molecules diffusing in ZIF-8: a short-time intra-cavity hopping process and a long-time inter-cavity hopping process. However, the framework flexibility is found to play a crucial role in determining the order of spatial arrangement and local structure, self-diffusion coefficient and reorientational dynamics of confined water. Specifically, the DREIDING force field gives rise to an unrealistic stiff framework, enhancing the order of spatial arrangement and diminishing the local ordered structure of confined water. Meanwhile, it results in much slower translational and reorientational dynamics. Hence, the general DREIDING force field cannot be considered for providing a quantitative description of the water structure and dynamics.

Interaction between PEO and Kaolinite in Flocculating: An Experimental and Molecular-Simulation Study

In this paper, the flocculation properties of polyethylene oxide (PEO) on kaolinite and the mechanism of adsorption on kaolinite anisotropic substrates were explored. As revealed by the experimental results, the settling rate and removal rate of kaolinite increased with increasing PEO concentration, but too high PEO concentration would cause the small particles to stabilize and become difficult to settle. Furthermore, to probe deep into the interactions between PEO and kaolinite anisotropic substrates, the morphology of adsorbed PEO, interfacial adsorption structure, and dynamic behavior of water molecules were determined by quartz crystal microbalance with dissipation (QCM-D) and molecular dynamics (MD) simulations. The adsorption amount of PEO on different mineral surfaces is in the order of kaolinite > alumina > silica, and the thickness of the adsorption structure formed by alumina is greater than that of silica. As illustrated by the MD simulation results, the adsorption of PEO reduces the concentration of water molecules attached to the kaolinite surface. The PEO forms a double-layer adsorption structure on the 001 surface, while forming a tight monolayer adsorption structure on the 001¯ surface, weakening the interaction between the surface and the water molecules. The above results demonstrate that the adsorption of PEO effectively weakened the hydration dispersion of kaolinite and promoted the agglomeration of kaolinite particles.

Investigation of dynamical properties of free water in hydroxypropyl cellulose–water mixture by PFG-NMR

The dynamical behavior of water molecules in hydroxypropyl cellulose (HPC)–water mixtures was observed by the pulse field gradient (PFG) NMR method. For a decay curve of the spin-echo signal intensity of a water proton peak, a contribution of the diffusional motion of free water is observed. The water content dependence of the NMR relaxation time and diffusion coefficient of free water shows characteristic behavior reflecting the isotropic-cholesteric phase transition of HPC. These parameters of free water obtained by PFG-NMR correlate strongly with the fast dynamics of free water observed in the GHz region, and this correlation is explained by dynamics of water constrained by the geometrical self-similarity formed by the HPC molecules.

Local Dynamics of the Hydration Water and Poly(Methyl Methacrylate) Chains in PMMA Networks.

The dynamic behavior of water molecules and polymer chains in a hydrated poly(methyl methacrylate) (PMMA) matrix containing a small amount of water molecules was investigated. Water molecules have been widely recognized as plasticizers for activating the segmental motion of polymer chains owing to their ability to reduce the glass transition temperature. In this study, combined with judicious hydrogen/deuterium labeling, we conducted quasi-elastic neutron scattering (QENS) experiments on PMMA for its dry and hydrated states. Our results clearly indicate that the dynamics of hydrated polymer chains are accelerated, and that individual water molecules are slower than bulk water. It is therefore suggested that the hydration water affects the local motion of PMMA and activates the local relaxation process known as restricted rotation, which is widely accepted to be generally insensitive to changes in the microenvironment.

New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study.

Human GMP reductase (hGMPR) enzyme is involved in a cellular metabolic pathway, converting GMP into IMP, and also it is an important target for anti-leukemic agents. Present computational investigations explain dynamical behavior of water molecules during the conformational transition process from GMP to IMP using molecular dynamics simulations. Residues at substrate-binding site of cancerous protein (PDB Id. 2C6Q) are mostly more dynamic in nature than the normal protein (PDB Id. 2BLE). Nineteen conserved water molecules are identified at the GMP/IMP binding site and are classified as (i) conserved stable dynamic and (ii) infrequent dynamic. Water molecules W11, W14, and W16 are classified as conserved stable dynamic due to their immobile character, whereas remaining water molecules (W1, W2, W3, W4, W5, W7, W8, W9, W10, W12, W13, W15, W17, W18, and W19) are infrequent with dynamic nature. Entrance or displacement of these infrequent water molecules at GMP/IMP sites may occur due to forward and backward movement of reference residues involving ligands. Four water molecules of hGMPR-I and nine water molecules of hGMPR-II are observed in repetitive transitions from GMP to IMP pathway, which indicates discrimination between two isoforms of hGMPRs. Water molecules in cancerous protein are more dynamic and unstable compared to normal protein. These water molecules execute rare dynamical events at GMP binding site and could assist in detailed understanding of conformational transitions that influence the hGMPR's biological functionality. The present study should be of interest to the experimental community engaged in leukemia research and drug discovery for CML cancer.

Aqueous Affinity and Interfacial Dynamics of Anisotropic Buckled Black Phosphorous

The structure of black phosphorous (BP) is similar to the honeycomb arrangement of graphene, but the layered BP is found to be buckled and highly anisotropic. The buckled surface structure affects interfacial molecule mobility and plays a vital role in various nanomaterial applications. The BP is also known for wettability, droplet formation, stability, and hydrophobicity in the aqueous environment. However, there is a gap concerning the structural and dynamical behavior of water molecules, which is available in abundance for other monoatomic and polyatomic two-dimensional (2D) materials. Motivated by the technological importance, we try to bridge the gap by explaining the surface anisotropy-facilitated behavior of water molecules on bilayer BP using classical and first principles molecular dynamics (MD) simulations. From our classical MD study, we find three distinct layers of water molecules. The water layer closest to the interface is L1, followed by L2 and L3/bulk perpendicular to the BP surface. Water molecules in the L1 layer experience some structural disintegration in hydrogen bond (HB) phenomena compared to the bulk. There is a loss of HB donor-acceptor count per water molecule. The average HB count decreases because of an elevated rate of HB formation and deformation; this would affect the dynamic properties in terms of HB lifetime. Therefore, we observe the reduced lifetime of HB in the layer in close contact with BP, which again complements our finding on the diffusion coefficient of water molecules in distinct layers. Water diffuses relatively faster with diffusion coefficient 3.25 × 10-9 m2 s-1 in L1, followed by L2 and L3. The BP layer shows moderate hydrophobic nature. Our results also indicate the anisotropic behavior as the diffusion along the x-direction is faster than that along the y-direction. The gap in the slope of the x and y components of mean-squared displacement (MSD) complements the pinning effect in an aqueous environment. We observe blue-shifted and red-shifted libration and O-H stretching modes from the calculated power spectra for the L1 water molecules compared to the L2 and L3 molecules from first principles MD simulations. Our analysis may help understand the physical phenomena that occur during the surface wetting of the predroplet formation process observed experimentally.

Dynamic behaviour of water molecules in heterogeneous free space formed in an epoxy resin.

Although an epoxy resin is a stable material, it absorbs moisture over a long period of time, causing deterioration of its material properties. We here applied a full-atomistic molecular dynamics (MD) simulation to study where water molecules exist in an epoxy resin and how they dynamically behave. First, the curing reaction was simulated to obtain a network structure so that the time course of the density, and thereby the free space, in the resin were obtained. The results made it possible to discuss the formation and size distribution of the free spaces which were not connected to each other. Then, a few percent of water were inserted into the free space of the cured epoxy resin to examine the location and dynamics of their molecules. We found that several water molecules were clustered at a preferred site, where hydrogen bonds can be formed with hydroxy, ether and amino groups of the network, in the free space, and they heterogeneously moved from there to other sites.

Interaction between STAC and coal/kaolinite in tailing dewatering: An experimental and molecular-simulation study

The presence of clay minerals in coal tailings leads to a significant deterioration during the dewatering process. In this study, a cationic surfactant, stearyl trimethyl ammonium chloride (STAC), was considered to enhance the dewatering efficiency of coal tailings. The effect of STAC on coal tailing dewatering was evaluated by the filtration test. Results indicate that STAC can reduce filter cake moisture by increasing the hydrophobicity of particles, decreasing the surface tension of the filtrate, as well as neutralizing the associated charge. Furthermore, to investigate the interactions between STAC and coal tailings, the morphology of adsorbed STAC, interfacial adsorption structure, and dynamic behavior of water molecules were determined by atomic force microscopy (AFM) and molecular dynamics (MD) simulations on an atomic scale. AFM results revealed that the morphologies of STAC adsorbed on coal and kaolinite surfaces differed, owing to distinct interaction mechanisms. The adsorption of STAC on the kaolinite 001 surface is more uniform than on the 001- face and is predominantly based on monolayer adsorption through electrostatic interactions and hydrogen bonding. The MD simulation results suggest that the adsorption of STAC significantly inhibits the attachment of water molecules on coal and kaolinite surfaces. The nitrogen atoms of STAC were adsorbed to the particle surface, such that its alkyl chains were oriented towards water, thereby weakening the interaction between the particles and water. The above findings indicate that the addition of STAC can improve the hydrophobicity of coal and kaolinite effectively and thus, enhance the dewatering performance of coal tailings.

Electric‐field penetration depth and dielectric spectroscopy observations of human skin

BackgroundThe dynamic behavior of water molecules remains an important subject for understanding human skin. The change in the dynamics of water molecules from those in bulk water can be effectively observed by dielectric spectroscopy. To study water in the human skin in vivo, non‐invasive and non‐destructive measurements are essential. Since many unknowns remain from previous research, in this report we employ a two‐layer dielectric model to evaluate the penetration depth of the electric field and use the results in measurements on human skin.Materials and MethodsWe used open‐ended coaxial probes with different diameters to perform time‐domain reflectometry (TDR) measurements for an acetone‐Teflon double‐layer model and for human skin from various parts of the body.ResultsThe electric‐field penetration depth obtained from model measurements increases with the increasing outer diameter of open‐ended coaxial electrodes. For skin measurements, the relaxation strength corresponding to the water content shows a clear dependence on the epidermal thickness of the measured body parts.ConclusionWe determined the depth distribution of the water content of skin from results of dielectric measurements obtained using electrodes with various electric‐field penetration depths. We found exponential decays with the thickness of the epidermis of each body part for several examinees. This study suggests an effective method for detailed evaluations of human skin.

Physical properties of tofu gel probed by water translational/rotational dynamics

The dynamic behavior of water molecules in tofu gels is observed using dielectric spectroscopy (DS) and pulsed field gradient nuclear magnetic resonance (PFG-NMR) methods. The breaking stress of tofu gels are dependent on the heating time, which affects the water structures characterized by the dielectric relaxation time, τ. On the other hand, the inhomogeneity of the gel structures decreases with increasing coagulant concentration was reflected as decreasing of the dielectric broadening parameter, β, that related for a fluctuation of the dynamic water structure. In addition, a decrease in the translational diffusion coefficient of water molecules is obtained with increasing coagulant concentration suggesting a reduction of the free space for the diffusional motion of water molecules. Negative correlations between the broadening parameter, β, and the inverse of diffusion coefficient, 1/D, are found in tofu gels and soymilk with distinct correlation coefficients of −0.95 and −0.87, respectively. These results suggest that water dynamics analysis and complementary analysis using DS and PFG-NMR measuring techniques can be an effective tool to evaluate food gel physical properties. Further these technique could also explain the molecular mechanisms of gel and liquid structures and properties via dynamic water structures.

Structural and dynamical characterization of water on the Au (100) and graphene surfaces: A molecular dynamics simulation approach.

The positioning, adsorption, and movement of water on substrates is dependent upon the chemical nature and arrangement of the atoms of the surface. Therefore the behavior of water molecules on a substrate is a reflection of properties of the surface. Based on this premise, graphene and gold substrates were chosen to study this subject from a molecular perspective. In this work, the structural and dynamical behaviors of a water nanodroplet on Au (100) and the graphene interfaces have been studied by molecular dynamics simulation. The results have shown how the structural and dynamical behaviors of water molecules at the interface reflect the characteristics of these surfaces. The results have demonstrated that residence time and hydrogen bonds' lifetime at the water-Au (100) interface are bigger than at the water-graphene interface. Energy contour map analysis indicates a more uniform surface energy on graphene than on the gold surface. The obtained results illustrate that water clusters on gold and graphene form tetramer and hexamer structures, respectively. Furthermore, the water molecules are more ordered on the gold surface than on graphene. The study of hydrogen bonds showed that the order, stability, and the number of hydrogen bonds is higher on the gold surface. The positioning pattern of water molecules is also similar to the arrangement of gold atoms while no regularity was observed on graphene. The study of dynamical behavior of water molecules revealed that the movement of water on gold is much less than on graphene which is in agreement with the strong water-gold interaction in comparison to the water-graphene interaction.

Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules.

In biological systems, structural confinements of amyloid fibrils can be mediated by the role of water molecules. However, the underlying effect of the dynamic behavior of water molecules on structural stabilities of amyloid fibrils is still unclear. By performing molecular dynamics simulations, we investigate the dynamic features and the effect of interior water molecules on conformations and mechanical characteristics of various amyloid fibrils. We find that a specific mechanism induced by the dynamic properties of interior water molecules can affect diffusion of water molecules inside amyloid fibrils, inducing their different structural stabilities. The conformation of amyloid fibrils induced by interior water molecules show the fibrils' different mechanical features. We elucidate the role of confined and movable interior water molecules in structural stabilities of various amyloid fibrils. Our results offer insights not only in further understanding of mechanical features of amyloids as mediated by water molecules, but also in the fine-tuning of the functional abilities of amyloid fibrils for applications.

First-principles calculations of the water molecules and hydroxylated iron surface

ABSTRACTTo provide atomic scale understanding of the initial corrosion process of Fe in aqueous environment, the electronic interaction of between water molecules and hydroxyl groups with the (110) and (100) surface of Fe is investigated in a density functional theory approach. Using periodic slab models, stable structures and electronic states are calculated, and the dynamical behavior of water molecules and hydroxylated iron surface under finite temperature is resolved by first-principles molecular dynamics. The position of hydroxyl groups on surface does not change from the initial bridge position, while water molecules move from the initial on-top to bridge site, and the molecular surface tilts from a parallel position, the hydrogen bonds are also formed between water molecules and hydroxyl groups. This result suggests that the interaction due to the hydrogen bonding is dominant.

Structural and Dynamical Properties of Water Molecules Confined within Clay Sediments Probed by Deuterium NMR Spectroscopy, Multiquanta Relaxometry, and Two-Time Stimulated Echo Attenuation

The structure and multiscale dynamics of water molecules confined within dense clay sediments are investigated by deuterium (2H) NMR spectroscopy, relaxometry, and two-time correlation measurements. The splitting of the 2H NMR resonance line quantifies the specific ordering of water molecules confined within the clay interlamellar space. The angular distribution of clay aggregates within the sediment is evaluated from variation of the transverse 2H NMR relaxation rates as a function of orientation of the clay film within the static magnetic field. The average residence time of the water molecules within clay aggregates is determined by multiquanta spin-locking relaxometry. Finally, water exchange between different aggregates is extracted from the attenuation of 2H two-time stimulated echo. These simultaneous NMR dynamical investigations cover a broad range of characteristic times (between 10 μs and 100 ms) appropriate to investigate the multiscale dynamical behavior of water molecules confined within hete...

Effect of Surface Passivation in Spinel Slurry Toward Hydrolysis: Neutron Scattering and Rheological Studies

Aqueous colloidal forming of magnesium aluminate (MgAl2O4) spinel offers much potential for various applications; however, these advantages are generally offset by the basic nature of the powder and its affinity for hydrolysis. Hydrolysis in the presence of water generally imparts surface chemical changes resulting in the degradation of colloidal stability. In the present study, spinel powders were subjected to thermally assisted surface passivation and evaluated for the effectiveness of preventing hydrolysis through quasielastic neutron scattering (QENS) technique and correlated with rheological measurements. In order to evaluate the extent of hydrolysis, spinel slurries prepared with (SP) and without surface passivation (WSP) were studied by rheological and QENS measurements at regular intervals of time. While WSP slurry exhibited a steep enhancement in viscosity from 1.02 to 19.4 Pa · s and fraction of the elastic intensity from 0.20 to 0.38 for 96 and 200 hours, respectively, a negligible change in viscosity for SP slurries from 0.313 to 0.345 Pa · s and fraction of the elastic intensity from 0.16 to 0.17 for the similar period confirmed the inhibition of hydrolysis, revealing change in surface chemistry due to hydrolysis. Microscopic details as obtained from neutron scattering data revealed that dynamical behavior of water molecules in both the slurries could be described very well by the Singwi–Sjolander model of jump diffusion. Further analysis showed lower diffusivity ∼1.82 × 10−5 cm2/sec and higher residence time ∼6.39 ps for WSP slurry in comparison with 2.16 × 10−5 cm2/sec and 5.80 ps, complimenting the inhibition of hydrolysis in case of SP slurry.

AOT逆ミセル内における水の構造および動的挙動の分子動力学解析

AOT逆ミセル内における水の構造および動的挙動の分子動力学解析

Pressure Effect on the Reorientational Correlation Time of Water in Formamide–Water Mixtures at 25 °C

Abstract NMR spin–lattice relaxation times (T1) for nucleus D of D2O in deuterated formamide (FA-d3)–D2O mixtures were measured up to 80 mol % of FA-d3 at 25 °C under pressure up to 196.1 MPa. To discuss the pressure effect on the dynamic behavior of water molecules in the mixtures, the reorientational correlation times (τc) of D2O molecules were estimated from the quadrupole coupling equation. τc monotonously increased with increasing FA-d3 content at all pressures studied. However, τc apparently decreased with increasing pressure until 20 mol % of FA-d3, while over 40 mol % of FA-d3 the pressure coefficient of τc (∂τc/∂P) became positive and larger with increasing FA-d3 content. A negative pressure coefficient would indicate the existence of three-dimensional hydrogen-bonded network structure of water, and a positive one would be ascribed to the strengthening of dipole interactions and hydrogen bonds between FA-d3 and D2O by compression. In order to investigate the pressure effect on the reorientational dynamics of water molecules in detail, we performed molecular dynamics (MD) simulations paying attention to the pressure effect on hydrogen-bonding and dipole interactions.

Pressure Effect on the Reorientational Correlation Time of Water in N,N-Dimethylformamide–Water Mixtures at 25 °C

Abstract NMR spin–lattice relaxation times (T1) for nucleus D of D2O in N,N-dimethylformamide (DMF)–D2O mixtures were measured up to 80 mol % of DMF at 25 °C under high pressure up to 196.1 MPa. To discuss the pressure effect on the dynamic behavior of water molecules in the mixtures, the reorientational correlation times (τc) of D2O molecules were estimated from the quadrupole coupling equation. τc in neat D2O decreased monotonously with increasing pressure and the negative pressure coefficient of τc (∂τc/∂P < 0) was still observed at 5 mol % of DMF, while ∂τc/∂P became positive at more than 10 mol % of DMF as in the cases of ordinary liquids and larger with increasing DMF content. These results would be ascribed to the diminishing of the effect of pressure-induced distortion of the hydrogen-bonded network of water. In order to investigate the pressure effect on the liquid structure and the reorientational dynamics of water molecules in detail, we performed the molecular dynamics (MD) simulations paying attention to the pressure effect on hydrogen-bonding, hydrophobic hydration, and dipole interaction.

Temperature Effect on the Reorientational Correlation Time of Water in Formamide– and N,N-Dimethylformamide–Water Mixtures

Abstract NMR spin–lattice relaxation times (T1) for nucleus D of D2O in FA-d3–D2O and DMF–D2O mixtures were measured up to 80 mol % of amide at 5, 25, and 45 °C under atmospheric pressure. To discuss the dynamic behavior of water molecules in the mixtures in detail, the reorientational correlation times (τc) of D2O molecules were estimated from the quadrupole coupling equation. In FA-d3–D2O mixtures, τc increased monotonously with increasing FA content at 25 and 45 °C, while we can recognize a shallow minimum at 5 °C in the D2O-rich region. In DMF–D2O mixtures, τc showed a remarkable maximum in the composition dependence at each temperature. In order to investigate the effect of the microscopic environments on the reorientational dynamics of water molecules, we calculated τc for individual environments through the MD simulations. From these results, we discussed the effects of hydrophilic and hydrophobic interactions on the molecular reorientational dynamics.

Structure-Based Prediction of the Mobility and Disorder of Water Molecules at Protein-DNA Interface

Water plays an invaluable role in governing the structure, stability, dynamics, and function of biomolecules, which has also been demonstrated to be critical in mediating biomolecular recognition and association. Accurate determination of the dynamic behavior of water molecules at biological complex interface is important for the understanding of the molecular mechanism of water contributing to the binding between biomolecules and could be exploited as an alternative tool to refine the water's positions in X-ray electron density map. In the present study, a method called local hydrophobic descriptors (LHDs) is used to characterize the hydrophobic landscapes of the hydration sites at protein-DNA interface. The resulting variables of the characterization are then correlated with the experimentally measured B-factor values of 4445 elaborately selected water samples derived from a panel of thematically nonredundant, high-quality protein-DNA interfaces by using a variety of machine learning methods, including PLS, BPNN, SVM, LSSVM, RF, and GP. The results show that the dynamic behavior of interfacial water molecules is primarily governed by the local hydrophobic feature of the hydration sites that water molecules located, and the nonlinear dependence dominates over the linear component in the water B-factor system. We expect that this structured-based approach can be used for predicting the B-factor profile of other biomolecules as well.