Average Number Of Water Molecules Research Articles

Exploration of the Existence Forms and Patterns of Dissolved Oxygen Molecules in Water

HighlightsA clear negative correlation between the size of water clusters and theconcentration of dissolved oxygen was observed. This implied that smaller clusters water exhibits higher concentrations of dissolved oxygen.Oxygen molecules are primarily existed at the surfaces or interfaces of waterclusters and can rapidly traverse the gas liquid interface.A semi empirical formula relating the average number of water molecules in acluster to 17O NMR half peak width was derived, demonstrating an approximatelin ear relationship.

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI‐SCS‐MP2/MM molecular dynamics simulation

AbstractThe spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd2+ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd2+. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd2+ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd2+ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.

On the influence of increasing the concentration of Au144(SRCOO1-)60 nanoparticles in water/Na1+ solution using molecular dynamics simulations

We performed molecular dynamics (MD) simulations in order to evaluate the effects of increasing the concentration of functionalized gold nanoparticles (AuNP), Au144(SC11H22COO1-)60 type, in water solution. Our results point to a formation of clusters in which each AuNP competes for regions with the others without reducing the average number of water molecules at the AuNP boundary. We also discuss how the direct interaction between the nanoparticle and the water molecules ends up being strengthened with the increase in the concentration of AuNPs, indicating an increase in the lifetime of the hydrogen bonds (HB) and in the limiting energy for the rupture of these HB between AuNP-water in the first solvation shell layer structure.

Structure of Aqueous KNO3 Solutions by Wide-Angle X-ray Scattering and Density Functional Theory.

The structure of aqueous KNO3 solutions was studied by wide-angle X-ray scattering (WAXS) and density functional theory (DFT). The interference functions were subjected to empirical potential structure refinement (EPSR) modeling to extract the detailed hydration structure information. In aqueous KNO3 solutions with a concentration from 0.50 to 2.72 mol·dm-3, water molecules coordinate K+ with a mean coordination number (CN) from 6.6 ± 0.9 to 5.8 ± 1.2, respectively, and a K-OW(H2O) distance of 2.82 Å. To further describe the hydration properties of K+, a hydration factor (fh) was defined based on the orientational angle between the water O-H vector and the ion-oxygen vector. The fh value obtained for K+ is 0.792, 0.787, 0.766, and 0.765, and the corresponding average hydration numbers (HN) are 5.2, 5.1, 4.8, and 4.5. The reduced HN is compensated by the direct binding of oxygen atoms of NO3- with the average CN from 0.3 ± 0.7 to 2.6 ± 1.7, respectively, and the K-ON(NO3-) distance of 2.82 Å. The average number of water molecules around NO3- slightly reduces from 10.5 ± 1.5 to 9.6 ± 1.7 with rN-OW = 3.63 Å. K+-NO3- ion association is characterized by K-ON and K-N pair correlation functions (PCFs). A K-N peak is observed at 3.81 Å as the main peak with a shoulder at 3.42 Å in gK-N(r). This finding indicates that two occupancy sites are available for K+, i.e., the edge-shared bidentate (BCIP) and the corner-shared monodentate (MCIP) contact ion pairs. The structure and stability of the KNO3(H2O)10 cluster were investigated by a DFT method and cross-checked with the results from WAXS.

Towards the correct microscopic structure of aqueous CsCl solutions with a comparison of classical interatomic potential models

The structure of aqueous CsCl solutions was investigated by classical molecular dynamics simulations (MD) at three salt concentrations (1.5, 7.5, and 15 mol %). Thirty interatomic potential sets, based on the 12–6 Lennard-Jones model, parametrized for non-polarizable water solvent molecules were collected and tested. Some basic properties, such as density, static dielectric constant, and self-diffusion coefficients, predicted by the force fields (FF), were compared with available experimental data. The simulated particle configurations were used to calculate the partial radial distribution functions (PRDF) and the neutron and X-ray total scattering structure factors (TSSF). The TSSFs were compared with experimental data from the literature, to find the best FF models, which describe the structure correctly.It was found that, though several of the thirty models failed in the tests, some models are compatible with the measured data. Values of the structural parameters consistent with the experiments were determined (such as water-ion distances, the average number of water molecules around the ions, average number, and distance between anion-cation contact ion pairs, water-water hydrogen bonds). It was shown, that in addition to models in which the number of contact ion pairs is too high, models in which this number is too low are also unable to reproduce the experimental data.

Insight into the self-aggregation behavior of lignite and anthracite in water: Atomic-level research using experiments and molecular dynamics simulations

To enable effective treatment of coal slime and prevent its release as an environmental pollutant, the interaction between coal particles in aqueous solutions must be well understood to enhance flocculation and sedimentation of the coal. In this study, the interaction between coal particles was explored using experiments and molecular simulations, which revealed the self-aggregation behavior of lignite and anthracite at different coalification levels in water. Atomic force microscopy results indicated that the anthracite–anthracite adhesion force is greater than that of lignite–lignite, and the adhesion force dominates particle interactions. The surface electrostatic potential range of lignite (-85.57–87.67 kcal/mol) is much higher than that of anthracite (-63.68–59.60 kcal/mol) and the lignite surface provides more polar regions for adsorbing water molecules. Lignite and anthracite rely on π–π accumulation to form a dimer skeleton structure. The dispersion interaction, dominated by π–π interactions, is key to promoting cluster formation and maintaining a stable cluster. The coal molecules proceed through three stages of movement, forming a cluster structure by dissipating the surrounding water molecules. The hydrophobic surface of the cluster molecules is exposed, gradually concealing the hydrophilic groups, which maintains the stability of coal self-aggregates. This process affects the water-molecule distribution, damaging the water bridge structure formed between the water molecules in coal molecule interlayers. This results in a decrease in the average number of water molecules surrounding a single lignite or anthracite molecule, and a change in the water-molecule orientation. Therefore, to enhance the flocculation of coal particles in slime water, it is necessary to increase the hydrophobicity of low-rank coal particles.

First-Principles Simulations of CuCl in High-Temperature Water Vapor.

Experimental data suggest that the solubility of copper in high-temperature water vapor is controlled by the formation of hydrated clusters of the form CuCl(H2O)n, where the average number of water molecules in the cluster generally increases with increasing density [Migdisov, A. A.; et al. Geochim. Cosmochim. Acta 2014, 129, 33-53]. However, the precise nature of these clusters is difficult to probe experimentally. Moreover, there are some discrepancies between experimental estimates of average cluster size and prior simulation work [Mei, Y. Geofluids 2018, 2018, 4279124]. We have performed first-principles Monte Carlo (MC) and molecular dynamics (MD) simulations to explore these clusters in finer detail. We find that molecular dynamics is not the most appropriate technique for studying aggregation in vapor phases, even at relatively high temperatures. Specifically, our MD simulations exhibit substantial problems in adequately sampling the equilibrium cluster size distribution. In contrast, MC simulations with specialized cluster moves are able to accurately sample the phase space of hydrogen-bonding vapors. At all densities, we find a stable, slightly distorted linear H2O-Cu-Cl structure, which is in agreement with the earlier simulations, surrounded by a variable number of water molecules. The surrounding water molecules do not form a well-defined second solvation shell but rather a loose network of hydrogen-bonded water with molecular CuCl on the outside edge of the water cluster. We also find a broad distribution of hydration numbers, especially at higher densities. In contrast to previous simulation work but in agreement with experimental data, we find that the average hydration number substantially increases with increasing density. Moreover, the value of the hydration number depends on the choice of cluster definition.

Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water?

We examine the ability of six molecular dynamics (MD) force fields (Amber ff14SB, Amber ff99SBnmr1, Amber ff03ws, OPLS-AA/L, OPLS-AA/M, and CHARMM36) to reproduce conformational ensembles of the central alanine in GAG and AAA in a way that is consistent with five (GAG) or six (AAA) J coupling constants and amide I' profiles. MD-derived Ramachandran plots for all six force fields under study differ from those obtained by the Gaussian fit to experimental data in three major ways: (i) the polyproline II (pPII) basin in the Ramachandran plot is too concentrated, (ii) the antiparallel β (aβ) basin is overpopulated, and (iii) the transitional β (βt) basin is underpopulated. Amber ff14SB outperforms the other five MD force fields and yields the highest pPII populations of the central alanine residue in GAG (55%) and AAA (63%), in good agreement with the predictions of the Gaussian model (59 and 76%). The analysis of the hydration layer around the central alanine residue reveals considerable reorientation of water molecules and reduction in both the average number of water molecules and the average number of water-water hydrogen bonds when glycines (in GAG) are replaced by alanines (in AAA), elucidating water-mediated nearest neighbor effects on alanine's conformational dynamics.

Molecular Modeling of Structure and Dynamics of Nafion Protonation States.

We present the results of the atomistic molecular dynamics modeling of different protonation states of Nafion at varying hydration levels. Previous experiments have shown that the degree of deprotonation (DDP) of the sulfonic acid groups in a Nafion membrane varies significantly upon hydration. Our goal is to provide insights into the effects of variable protonation states and water content on the internal structure and vehicular transport inside the Nafion membrane. The Nafion side chain lengths showed a weak increasing trend with increasing DDP at all hydration levels, exposing more of the sulfonic acid groups to the hydrophilic/water phase. The water-phase characteristic size/diameter decreased with increasing DDP, but, interestingly, the average number of water molecules per cluster increased. The probability of water–hydronium hydrogen bond formation decreased with increasing DDP, despite an increase in the total number of such hydrogen bonds. The water diffusion was largely unaffected by the state of deprotonation. In contrast to that, the hydronium ion diffusion slowed down with increasing DDP in the overall membrane. The hydronium ion residence times around the sulfonic acid group increased with increasing DDP. Our simulations show a strong connection between the morphology of the water domains and protonation states of Nafion. Such a connection can also be expected in polyelectrolyte membranes similar to Nafion.

Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.

We investigate the effect of solvent models on the computed thermodynamics of protein folding. Atomistic folding simulations of a fast-folding mini-protein, CLN025, were employed to compare two commonly used explicit solvent water models, TIP3P and TIP4P/Ew, and one implicit solvent (AMBER generalized Born) model. Although all three solvent models correctly identify the same native folded state (RMSD = 1.5 ± 0.1 Å relative to the experimental structure), the corresponding free energy landscapes vary drastically between water models: almost an order-of-magnitude difference is seen in the predicted fraction of the unfolded state between the two explicit solvent models, with even larger differences between the implicit and the explicit models. Quantitative arguments are presented for why the sensitivity is expected to hold for other proteins, as well as for other conformational transitions involving large changes in solvent exposed areas such as protein-ligand binding. Comparing protein-solvent and solvent-solvent contributions to the folding energy between different water models, water-water electrostatic interactions are identified as the largest contributor to the differences in the predicted folding energy, which helps explain the strong sensitivity of the folding landscape to subtle details of the water model. For the two explicit solvent models, differences in water model parameters also result in the average number of water molecules surrounding the protein being noticeably different. Water models that poorly reproduce certain bulk properties of liquid water such as self-diffusion are likely to misrepresent water-water interactions; we argue that within a pairwise additive energy function this error cannot, in general, be compensated by an adjustment to the solute-solute and solute-solvent parts of the energy.

Models for the Immediate Environment of Ions in Aqueous Solutions of Neodymium Chloride

Radial distribution functions of neodymium chloride aqueous solutions in a wide range of concentrations under ambient conditions are calculated from experimental data obtained earlier via X-ray diffraction analysis. Different models of the structural organization of the system are developed. The optimum versions are determined by calculating theoretical functions for each model and comparing their fit to the experimental functions. Such quantitative characteristics of the immediate environment of Nd3+ and Cl− ions as coordination numbers, interparticle distances, and varieties of ion pairs are determined. It is shown that the average number of water molecules in the first coordination sphere of the cation falls from 9 to 6.2 as the concentration rises. The structure of the systems over the whole range of concentrations is determined by ion associates of the noncontact type.

Structural parameters of the nearest environment of ions in aqueous solutions of ytterbium chloride

The radial distribution functions (RDFs) of aqueous solutions of ytterbium chloride were calculated using previously collected X-ray diffraction data for a wide range of solution concentrations under ambient conditions. Different solution structure models were constructed. Theoretical RDFs were calculated for each model. The optimum models for all systems studied were chosen based on the best fit between the theoretical and experimental RDFs. Quantitative characteristics of the nearest environment of Yb3+ and Cl– ions in solutions, namely, the coordination number, interparticle distances, and types of ion pairs were determined. The average number of water molecules in the first coordination sphere of the cation decreases from 8.2 to 6.0 as the solution concentration increases. The structure of all systems investigated is governed by non-contact ion associates throughout the concentration range studied.

Hydration of copper(II) amino acids complexes.

Hydration of the copper(II) bis-complexes with glycine, serine, lysine, and aspartic acid was studied by DFT and MD simulation methods. The distances between copper(II) and water molecules in the 1st and 2nd coordination shells, the average number of water molecules and their mean residence times in the hydration shells were calculated. Good agreement was observed between the values obtained and those found by DFT and NMR relaxation methods. Influence of the functional groups of the ligands and the cis-trans isomerism of the complexes on the structural and dynamical parameters of the hydration shells was displayed and explained. Analysis of the MD trajectories reveals the competition for a copper(II) axial position between water molecules or water molecules and the functional chain groups of the ligands and confirms the suggestion on the pentacoordination of copper(II) in such complexes. MD simulations show that only one axial position of Cu(II) is basically occupied at each time step while in average the coordination number more than 5 is observed. © 2017 Wiley Periodicals, Inc.

Coordination of ions in aqueous solutions of samarium chloride from X-ray diffraction data

The radial distribution functions for aqueous solutions of samarium chloride over a broad concentration range under standard conditions, obtained previously by X-ray diffraction, were used to develop various physically substantiated models for structural organization of the systems. The optimal versions were identified by calculating the theoretical functions for each model and comparing their agreement with experimental functions. The quantitative characteristics of the local environment of Sm3+ and Cl– ions such as coordination numbers, interparticle distances, and sorts of ion pairs were established. The average number of water molecules in the first coordination sphere of the cation was found to decrease from 9 to 6 with increasing concentration. The structure of the systems is determined by solvent-separated ion associates over the whole concentration range.

B(OH)4- hydration and association in sodium metaborate solutions by X-ray diffraction and empirical potential structure refinement.

X-ray diffraction is used to study the structure of aqueous sodium metaborate solutions at salt concentrations of 1, 3, and 5 (oversaturated) mol dm-3. The X-ray structure factors are subjected to empirical potential structure refinement (EPSR) modelling to extract the individual site-site pair correlation functions, the coordination numbers, and the spatial density functions (three-dimensional structure) of ion hydration and association as well as solvent water in the borate solutions. The sodium ion is surrounded on average by (5.4 ± 0.7), (4.6 ± 1.0), and (3.7 ± 1.2) water molecules at 1, 3, and 5 mol dm-3, respectively, with the Na-O (H2O) distance of 2.34 Å. The decrease in hydration number of the sodium ion is compensated by direct binding of the oxygen atom of the borate ion, B(OH)4-, with the average coordination number of (0.2 ± 0.5), (1.0 ± 0.8), and (2.1 ± 1.3) at the Na-O(B) distance of 2.34 Å to keep the octahedral hydration shell of the sodium ion. The average number of water molecules around the borate ion is (13.9 ± 1.8), (14.2 ± 1.8), and (16.1 ± 2.4) per borate ion with increasing salt concentration with the B-O(H2O) distance of 3.72 Å. The number of nearest-neighbour water molecules around a central water molecule in a solvent decreases as (4.8 ± 1.2), (3.8 ± 1.1), and (2.8 ± 1.1) with an increase in salt concentration with the O(H2O)-O(H2O) distance of 2.79 Å. The Na+-B(OH)4- ion association is characterized by the Na-O(B) and Na-B pair correlation functions. The Na-B interactions are observed at 3.00 Å as a shoulder and 3.57 Å as a main peak in the site-site pair correlation function, suggesting two occupancy sites of Na+ with one for the edge-shared bidentate bonding and the other for the corner-shared monodentate bonding. The total number of Na-B interactions at 3.00 and 3.57 Å is consistent with that of the Na-O(B) interactions. The detailed three-dimensional structure of the ion hydration and association is visualized as a function of salt concentration. The structure and stability of [NaB(OH)4(H2O)6]0 clusters are further investigated by DFT calculations, and the most likely structure is proposed and cross-checked.

Dynamical aspects of water-poly(ethylene glycol) solutions studied by 1H NMR

This paper describes the results of a detailed investigation on the dynamic behavior of poly(ethylene glycol), PEG, with low molar mass (200, 300, 400 and 600gmol−1) and water in all ranges of concentrations. The study is based on spin–spin (T2), spin–lattice (T1) relaxation times and on the variations of the proton chemical shift. The relaxations of the exchangeable and non-exchangeable hydrogen atoms depend on the mobility of the molecules of the solutions. Therefore, the results of T1 and T2 allow one to determine the transitions between the dilute, semi-dilute and concentrate polymeric regimes, and they were well correlated with the kinematic viscosity of the solutions. The distribution of water molecules between the ethylene oxide and the terminal hydroxyl groups of PEG in the entire regime was investigated by using high-field NMR, and the characteristic average number of water molecules belonging to the hydration layer of PEG was also determined.

Models of the nearest surrounding of ions in aqueous solutions of dysprosium chloride

Structural organization models are developed using radial distribution functions obtained earlier via XRD analysis for aqueous solutions of dysprosium chloride over a wide range of concentrations under standard conditions. The optimum variants are selected by calculating the theoretical functions for each model and comparing how they agree with experimental functions. Quantitative characteristics of the nearest surrounding of Dy3+ and Cl– ions, e.g., coordination numbers, interparticle distances, and varieties of ion pairs, are established. It is shown that the average number of water molecules in the first coordination sphere of a cation falls from 8.5 to 6 as the concentration grows; the structure of the system over the range of concentrations is determined by noncontact ion associates.

Chain length dependent alkane/β-cyclodextrin nonamphiphilic supramolecular building blocks.

In this work we report the chain length dependent behavior of the nonamphiphilic supramolecular building blocks based on the host-guest inclusion complexes of alkanes and β-cyclodextrins (β-CD). (1)H NMR, ESI-MS, and SAXS measurements verified that upon increasing the chain length of alkanes, the building blocks for vesicle formation changed from channel type 2alkane@2β-CD via channel type alkane@2β-CD to non-channel type 2alkane@2β-CD. FT-IR and TGA experiments indicated that hydrogen bonding is the extensive driving force for vesicle formation. It revealed that water molecules are involved in vesicle formation in the form of structural water. Upon changing the chain length, the average number of water molecules associated with per building block is about 16-21, depending on the chain length.

Xe affinities of water-soluble cryptophanes and the role of confined water.

Given their relevance to drug design and chemical sensing, host-guest interactions are of broad interest in molecular science. Natural and synthetic host molecules provide vehicles for understanding selective molecular recognition in aqueous solution. Here, cryptophane-Xe host-guest systems are considered in aqueous media as a model molecular system that also has important applications. 129Xe-cryptophane systems can be used in the creation of biosensors and powerful contrast agents for magnetic resonance imaging applications. Detailed molecular information on the determinants of Xe affinity is difficult to obtain experimentally. Thus, molecular simulation and free energy perturbation methods were applied to estimate the affinities of Xe for six water-soluble cryptophanes. The calculated affinities correlated well with the previously measured experimental values. The simulations provided molecular insight on the differences in affinities and the roles of conformational fluctuations, solvent, and counter ions on Xe binding to these host molecules. Displacement of confined water from the host interior cavity is a key component of the binding equilibrium, and the average number of water molecules within the host cavity is correlated with the free energy of Xe binding to the different cryptophanes. The findings highlight roles for molecular simulation and design in modulating the relative strengths of host-guest and host-solvent interactions.

Water transport through functionalized nanotubes with tunable hydrophobicity.

Molecular dynamics simulations are used to study the occupancy and flow of water through nanotubes comprised of hydrophobic and hydrophilic atoms, which are arranged on a honeycomb lattice to mimic functionalized carbon nanotubes (CNTs). We consider single-file motion of TIP3P water through narrow channels of (6,6) CNTs with varying fractions (f) of hydrophilic atoms. Various arrangements of hydrophilic atoms are used to create heterogeneous nanotubes with separate hydrophobic/hydrophilic domains along the tube as well as random mixtures of the two types of atoms. The water occupancy inside the nanotube channel is found to vary nonlinearly as a function of f, and a small fraction of hydrophilic atoms (f ≈ 0.4) are sufficient to induce spontaneous and continuous filling of the nanotube. Interestingly, the average number of water molecules inside the channel and water flux through the nanotube are less sensitive to the specific arrangement of hydrophilic atoms than to the fraction, f. Two different regimes are observed for the water flux dependence on f - an approximately linear increase in flux as a function of f for f < 0.4, and almost no change in flux for higher f values, similar to the change in water occupancy. We are able to define an effective interaction strength between nanotube atoms and water's oxygen, based on a linear combination of interaction strengths between hydrophobic and hydrophilic nanotube atoms and water, that can quantitatively capture the observed behavior.