Clusters Of Water Molecules Research Articles

High-Level Ab Initio Predictions of the Energetics of mCO2·(H2O)n (n = 1–3, m = 1–12) Clusters

Electronic structure calculations at the correlated molecular orbital theory and density functional theory levels have been used to generate a reliable set of clustering energies for up to three water molecules in carbon dioxide clusters up to n = 12. The structures and energetics are dominated by Lewis acid-base interactions with hydrogen-bonding interactions playing a lesser energetic role. The actual binding energies are somewhat larger than might be expected. The correlated molecular orbital MP2 method and density functional theory with the ωB97X exchange-correlation functional provide good results for the energetics of the clusters, but the B3LYP and ωB97X-D functionals do not. Seven CO(2) molecules form the first solvent shell about a single H(2)O with four CO(2) molecules interacting with the H(2)O via Lewis acid-base interactions, two CO(2) interacting with the H(2)O by hydrogen bonds, and the seventh CO(2) completing the shell. The Lewis acid-base and weak hydrogen bond interactions between the water molecules and the CO(2) molecules are strong enough to disrupt the trimer ring configuration for as few as seven CO(2) molecules. Calculated (13)C NMR chemical shifts for mCO(2)·(H(2)O)(n) show little change with respect to the number of H(2)O or CO(2) molecules in the cluster. The O-H stretching frequencies do exhibit shifts that can provide information about the interactions between water and CO(2) molecules.

Water vapor sorption and free volume in the aromatic polyamide layer of reverse osmosis membranes

Thin film composite membranes consist of an ultra thin active layer of polymer that governs the membrane's salt rejection and water permeation properties. However, the fragility of the ultrathin layer makes it challenging to select a technique capable of differentiating between the properties of this layer from the supporting layer. In this study, we isolated enough active layer material to characterise the water vapour sorption and free volume cavity size as functions of water activity. The sorption data were modelled using the Guggenheim–Anderson–De Boer (G.A.B.) isotherm and from this the number of sorption sites for water was calculated to be 189×1019 per gram for the active layer from a commercial Dow Filmtec SW30 membrane and 188×1019 per gram for an aromatic polyamide material prepared in house. The activation energy for diffusion of water through the active layer of SW30 was also evaluated and found to be 6.95kcal/mol, lower than the heat of liquefaction of water. This suggests that water does not permeate as individual molecules in the vapour state, but rather as clusters of water molecules. The free volume cavity size in the active layer as a function of moisture uptake was also investigated and the results were explained using a pore filling and pore swelling mechanism. This study sheds light on the mechanisms of water entry into the active layer, water transport through the active layer, and the corresponding response of the polymer chains, thereby giving critical insight for the development of more novel systems.

Ab initio study of water clustering in the presence of a methyl radical

The geometrical structure and binding energy of small clusters of methyl radical and water molecules (up to five water molecules) in gas phase and water media have been investigated at the MP2 level of theory using 6-311++G(2df,2p) basis set. The complexes characterized contain OH···O, CH···O, and OH···C attractive interactions with stabilization energies in the range 6–143 kJ mol−1. The solvent has an enhancing influence on the stabilities of studied clusters. The atoms in molecules theory were also applied to explain the nature of the complexes. The interaction energies have been partitioned with the natural energy decomposition analysis showing that the most important attractive term corresponds to the charge transfer one.

Sialyl Lewisx: A “Pre‐Organized Water Oligomer”?

Organized and released: Sialyl Lewis(x) (sLe(x)) represents a "pre-organized water oligomer", that is, a surrogate for clustered water molecules attached to a scaffold. The impetus for sLe(x) binding to E-selectin is shown to be the high degree of pre-organization allowing an array of directed hydrogen bonds, and the entropic benefit of the release of water molecules from the large binding interface to bulk water (see picture).

Cover Picture: Sialyl Lewisx: A “Pre-Organized Water Oligomer”? (Angew. Chem. Int. Ed. 29/2012)

A surrogate for clustered water molecules attached to a scaffold is how the “pre-organized water oligomer” sialyl Lewisx can be described. The impetus for its binding to E-selectin is investigated by B. Ernst et al. in their Communication on page 7327 ff. Using isothermal titration calorimetry they show the key factors are the high degree of pre-organization allowing an array of directed hydrogen bonds, and the entropic benefit on releasing water molecules from the large binding interface.

A new model for water adsorption in porous ceramics

This research proposes a new isotherm model that is derived for adsorption of clustering and condensable vapors on mesoporous ceramics. The adsorption characteristics of water vapor on both experimental data and isotherm model were investigated over the relative pressure ranging from 0 to 0.95. The applicability of the model was evaluated by significance of fitting parameters. For each adsorption isotherm there are five parameters (m, qf, Kf, qm and Km). The comparison of modeling fit with experimental data was used as the methodology for selecting the most informative and the best-fitting model. The experimental testing results showed that this model is able to describe all possible behaviors of the water adsorption isotherm displaying type IV classification. The model is based on the forming and growth of the water molecule clusters and capillary condensation mechanism in mesopore. The findings suggest a significant tool for understanding the behavior of water adsorption in humidity-control porous ceramics.

Calorimetric and relaxation properties of xylitol-water mixtures

We present the first broadband dielectric spectroscopy (BDS) and differential scanning calorimetry study of supercooled xylitol-water mixtures in the whole concentration range and in wide frequency (10(-2)-10(6) Hz) and temperature (120-365 K) ranges. The calorimetric glass transition, T(g), decreases from 247 K for pure xylitol to about 181 K at a water concentration of approximately 37 wt. %. At water concentrations in the range 29-35 wt. % a plentiful calorimetric behaviour is observed. In addition to the glass transition, almost simultaneous crystallization and melting events occurring around 230-240 K. At higher water concentrations ice is formed during cooling and the glass transition temperature increases to a steady value of about 200 K for all higher water concentrations. This T(g) corresponds to an unfrozen xylitol-water solution containing 20 wt. % water. In addition to the true glass transition we also observed a glass transition-like feature at 220 K for all the ice containing samples. However, this feature is more likely due to ice dissolution [A. Inaba and O. Andersson, Thermochim. Acta, 461, 44 (2007)]. In the case of the BDS measurements the presence of water clearly has an effect on both the cooperative α-relaxation and the secondary β-relaxation. The α-relaxation shows a non-Arrhenius temperature dependence and becomes faster with increasing concentration of water. The fragility of the solutions, determined by the temperature dependence of the α-relaxation close to the dynamic glass transition, decreases with increasing water content up to about 26 wt. % water, where ice starts to form. This decrease in fragility with increasing water content is most likely caused by the increasing density of hydrogen bonds, forming a network-like structure in the deeply supercooled regime. The intensity of the secondary β-relaxation of xylitol decreases noticeably already at a water content of 2 wt. %, and at a water content above 5 wt. % it has been replaced by a considerably stronger water (w) relaxation at about the same frequency. However, the similarities in time scale and activation energy between the w-relaxation and the β-relaxation of xylitol at water contents below 13 wt. % suggest that the w-relaxation is governed, in some way, by the β-relaxation of xylitol, since clusters of water molecules are rare at these water concentrations. At higher water concentrations the intensity and relaxation rate of the w-relaxation increase rapidly with increasing water content (up to the concentration where ice starts to form), most likely due to a rapid increase of small water clusters where an increasing number of water molecules interacting with other water molecules.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these "slow" water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Investigation of Methanol–Peptide Nuclear Overhauser Effects through Molecular Dynamics Simulations

Intermolecular nuclear Overhauser effects (NOEs) produced by interactions of methanol with [val(5)]angiotensin in 25% methanol-water at 0 °C were examined through molecular dynamics (MD) simulations and compared to experimental results. Calculated average (3)J(NHCαH) spin coupling constants, conformation-sensitive chemical shift changes, and intramolecular (1)H-(1)H NOEs indicated that peptide conformations present over the course of simulation trajectories of 100-300 ns are likely similar to those present in the experimental system. Calculated cross-relaxation terms for the methanol-peptide interactions showed the same trends as corresponding experimental data but were about a factor of 3 too large. The lack of agreement between observed and calculated cross-relaxation terms probably has origins in characteristics of the simulations that lead to overestimation of translational diffusion coefficients of the system components. Simulations confirmed the heterogeneity of the methanol-water solvent at the molecular level, with clusters of methanol and water molecules changing their size and composition on a subpicosecond time scale. Most peptide hydrogens are preferentially solvated by interactions with methanol molecules. Simulations suggest that diffusion of water and methanol molecules near the peptide is slowed as these species approach the peptide backbone.

Formation of water and glucose clusters by hydrogen bonds in glucose aqueous solutions

Glucose aqueous solutions with different concentrations have been studied using molecular dynamics simulation methods to analyze hydrogen bond clusters. Density profiles analysis revealed that there is local clustering of glucose and water molecules in the higher concentration systems. Hydrogen bonds analysis found that as glucose concentration increases, the glucose–water and glucose–glucose hydrogen bond interactions increase. Percolation analysis showed that the percolation threshold for water clusters is around 0.151. The percolation threshold for glucose clusters has also been discussed.

Hydrogen-bonded network of hydration water around model solutes

Clustering of water molecules in the hydration shells of spherical structureless solutes was studied in dependence on thermodynamic state, solute radius R(sp) and strength U(0) of water-solute interaction. Two qualitatively different clustering states of hydration water have been found: an "ordered" state with a hydrogen-bonded (H-bonded) network, which includes most of the hydration water, and a "disordered" state with small H-bonded clusters of hydration water. The transition from the ordered to disordered state occurs upon increasing temperature and decreasing pressure. This percolation transition is rounded due to the finite solute size and occurs in some temperature (pressure) interval. A finite-size scaling was applied to determine the transition temperature T(∞) in the limit R(sp)→∞. Strengthening of the water-solute interaction strongly enhances the stability of the ordered state: the transition temperature increases by about 35 °C, when U(0) decreases by 1 kcal mol(-1). At T > T(∞) and fixed U(0), the stability of the H-bonded water network increases upon decreasing solute size.

2116 大規模な水分子クラスターの外部電場に対する時間応答に関する剛体動力学シミュレーション(OS21-4.固体物理/流体物理のマルチフィジックス/マルチスケール解析(4),OS・一般セッション講演)

2116 大規模な水分子クラスターの外部電場に対する時間応答に関する剛体動力学シミュレーション(OS21-4.固体物理/流体物理のマルチフィジックス/マルチスケール解析(4),OS・一般セッション講演)

Water transport and clustering behavior in homopolymer and graft copolymer polylactide

Polylactide is a bio-based and biodegradable polymer well-known for its renewable origins. Water sorption and clustering behavior in both a homopolymer polylactide and a graft copolymer of polylactide was studied using the quartz crystal microbalance/heat conduction calorimetry (QCM/HCC) technique. The graft copolymer, poly(1,5-cyclooctadiene-co-5-norbornene-2-methanol-graft-d,l-lactide), contained polylactide chains (95wt.%) grafted onto a hydrophobic rubbery backbone (5wt.%). Clustering is an important phenomenon in the study of water transport properties in polymers since the presence of water clusters can affect the water diffusivity. The HCC method using the thermal power signals and Van’t Hoff's law were both employed to estimate the water sorption enthalpy. Sorption enthalpy of water in both polymers was determined to be approximately −40kJ/mol for all water activity levels. Zimm–Lundberg analysis showed that water clusters start to form at a water activity of 0.4. The engaged species induced clustering (ENSIC) model was used to curve fit sorption isotherms and showed that the affinity among water molecules is higher than that between water molecules and polymer chains. All the methods used indicate that clustering of water molecules exists in both polymers.

Short Hydrogen Bond between Redox-Active Tyrosine YZand D1-His190 in the Photosystem II Crystal Structure

The crystal structure of photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed a remarkably short H-bond between redox-active tyrosine Y(Z) and D1-His190 (2.46 Å donor-acceptor distance). Using large-scale quantum mechanical/molecular mechanical (QM/MM) calculations with the explicit PSII protein environment, we were able to reproduce this remarkably short H-bond in the original geometry of the crystal structure in the neutral [Y(Z)O···H···N(ε)-His-N(δ)H···O═Asn] state, but not in the oxidized states, indicating that the neutral state was the one observed in the crystal structure. In addition to the appropriate redox/protonation state of Y(Z) and D1-His190, we found that the presence of a cluster of water molecules played a key role in shortening the distance between Y(Z) and D1-His190. The orientations of the water molecules in the cluster were energetically stabilized by the highly polarized PSII protein environment, where the Ca ion of the oxygen-evolving complex (OEC) and the OEC ligand D1-Glu189 were also involved.

Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles

To probe structural changes that occur when a membrane protein is transferred from lipid bilayers to SDS micelles, a fragment of bacteriorhodopsin containing transmembrane helical segments A and B was studied by fluorescence spectroscopy, molecular dynamics (MD) simulation, and stopped flow kinetics. In lipid bilayers, Förster resonance energy transfer (FRET) was observed between tyrosine 57 on helix B and tryptophans 10 and 12 on helix A. FRET efficiency decreased substantially when the peptide was transferred to SDS. MD simulation showed no evidence for significant disruption of helix–helix interactions in SDS micelles. However, a cluster of water molecules was observed to form a hydrogen-bonded network with the phenolic hydroxyl group of tyrosine 57, which probably causes the disappearance of tyrosine-to-tryptophan FRET in SDS. The tryptophan quantum yield decreased in SDS, and the change occurred at nearly the same rate as membrane solubilization. The results provide a clear example of the importance of corroborating distance changes inferred from FRET by using complementary methods.

Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins

Frequency-resolved communication maps provide a coarse-grained picture of energy transport in nanoscale systems. We calculate communication maps for homodimeric hemoglobin from Scapharca inaequivalvis and sample them to elucidate energy transfer pathways between the binding sites and other parts of the protein with focus on the role of the cluster of water molecules at the interface between the globules. We complement analysis of communication maps with molecular simulations of energy flow. Both approaches reveal that excess energy in one heme flows mainly to regions of the interface where early hydrogen bond rearrangements occur in the allosteric transition. In particular, energy is carried disproportionately by the water molecules, consistent with the larger thermal conductivity of water compared to proteins.

Effects of a low-intensity electromagnetic field on fibroblast migration and proliferation

The aim of this study was to test if an extremely weak 1 GHz electromagnetic field (EMF), known to be in resonance with clusters of water molecules, has biological effects on human fibroblasts. We demonstrated that in an in vitro model of wound healing, this EMF can activate fibroblast migration. [3H]thymidine incorporation experiments demonstrated that the EMF could also activate fibroblast proliferation. Activation of the expression of human fibroblast growth factor 1 (HFGF1) after EMF exposure showed that molecular wound healing pathways are activated in response to this water-resonant EMF.

A model SN2 reaction ‘on water’ does not show rate enhancement

Molecular dynamics calculations of the benchmark nucleophilic substitution reaction (SN2) Cl−+CH3Cl are carried out at the water liquid/vapor interface. The reaction free energy profile and the activation free energy are determined as a function of the reactants’ location normal to the surface. The activation free energy remains almost constant relative to that in bulk water, despite the fact that the barrier is expected to significantly decrease as the reaction is carried out near the vapor phase. We show that this is due to the combined effects of a clustering of water molecules around the nucleophile and a relatively weak hydration of the transition state.

Hydrogen bonding in aqueous solution of NaClO4

The ternary system NaClO4–H2O–D2O has been studied, using the Raman spectroscopy. Analysis of the uncoupled OD band of HDO clearly shows that the contour of the band consists of two components only. A new approach has been developed for the quantitative evaluation of the mole fraction of bonded OD groups as a function of perchlorate concentration. It is practically impossible to measure the absolute intensity of Raman scattering. Nevertheless, it is feasible to obtain the specific coefficients of scattering per bonded OD group from the ratio of integrated intensities of the components. For this purpose, the concept of negative ‘phantom’ concentration was introduced, at which all the OD groups must be bonded. As a result, the concentration dependence of the mole fraction of bonded OD groups has been derived. It was found that the infinite network of hydrogen bonds in bulk water ceases to exist at a mole fraction of NaClO4 above ∼0.03–0.035. At higher concentration of perchlorate only residual finite clusters of water molecules can take place. However, the infinite percolation in the system remains. The important fact resulting from the data treatment is that the average number of hydrogen bonds per water molecule in pure water is 2.6 ± 0.2.

HNO(H2O) n (n = 1–4) clusters: a theoretical study

The geometrical structure, binding energy, and vibrational spectra of small clusters of nitrosyl hydride (HNO) and water molecules, HNO(H2O)n, where (n = 1–4), have been investigated at the MP2 level of theory, using 6-311++G(2d,2p) basis set. We located three dimers, six trimers, nine tetramers, and three pentamers at the MP2/6-311++G(2d,2p) computational level. Particular attention is given to existence and magnitude of NH···O blue-shifting hydrogen bonds. Blue shifts of the NH stretching frequency upon complex formation in the ranges between 28 and 151 cm−1 is predicted. Cooperative effect in terms of stabilization energy along with the many-body interaction energies analysis was performed for the studied clusters. The Atoms in Molecules (AIM) theory was also applied to explain the nature of the complexes.