Bulk Water Molecules Research Articles

Correlation of reorientational jumps of water molecules in bulk water

Recent theoretical and experimental studies suggested the large-amplitude angular jump mechanism of the reorientational motions of water molecules. In this paper, we study the correlation effects of such angular jump motions, which are important for understanding a number of biological processes involving the motions of water molecules, by using molecular dynamics simulations. The results show that large-angular jump motions of a water molecule can enhance the successive jump motions of the same water molecule and the surrounding water molecules. Such a correlation can extend up to a distance of two water layers and is propagated through the perturbations to the local hydrogen bond networks. A detailed molecular picture of the correlation propagation is shown based on the molecular simulations.

Oxygen and Hydrogen Isotopic Preference in Hydration Spheres of Magnesium and Calcium Ions

Molecular orbital calculations were performed to estimate the 18O/16O and D/H isotopic reduced partition function ratios (rpfrs) of water molecules around magnesium and calcium ions. As model for water molecules in the ith hydration sphere of the cation in aqueous solutions containing that cation, we considered water molecules in the ith hydration sphere that were surrounded by water molecules in the (i+1)th hydration sphere in clusters, M2+(H2O)n (M = Mg or Ca; n up to 100). The calculations indicated that the decreasing order of the 18O preference over 16O in the primary hydration sphere is Mg2+ > Ca2+ > bulk water. That is, water molecules in the primary hydration spheres of the Mg2+ and Ca2+ ions are expected to be enriched in the heavier isotope of oxygen relative to water molecules in bulk, and the degree of the enrichment is larger for the Mg2+ ion than for the Ca2+ ion. No such preference was observed for hydrogen isotopes in any hydration sphere or for oxygen isotopes in the secondary and outer hydration spheres.

Molecular dynamics simulations of the condensation coefficient of water

Experiments have found the condensation coefficient for water condensing onto pure water to be between 1 and 0.01. This wide variation persists even in the more recent experiments in which values of about 1, 0.77±0.06, and 0.2±0.1 have been reported. However, current molecular dynamics simulations of water consistently result in a condensation coefficient of about 1. These water models may overestimate the condensation coefficient by assigning condensed phase parameters to the bulk, surface, and gas phase water molecules in the simulations. We varied the dipole moment and the Lennard-Jones parameters for a gas phase water molecule in a condensation simulation using the SPC/E model. With modest changes to the dipole moment and the Lennard-Jones parameters, we have obtained a value of 0.77. However, we have concluded that to obtain a simulation condensation coefficient of 0.2, unrealistic parameters must be assigned to the water molecules.

Oxygen and Hydrogen Isotopic Preference in Hydration Spheres of Chloride and Sulfate Ions

Abstract Molecular orbital calculations were performed to estimate the 18O/16O and D/H isotopic reduced partition function ratios (RPFRs) of water molecules around chloride and sulfate ions. Cl-(H2O) n and SO4 2-(H2O) n clusters with n up to 120 were considered as models of aqueous solution containing those anions. The calculations indicated that the decreasing order of the 18O preference over 16O in the primary hydration sphere is: (bulk water) > SO4 2- > Cl-. That is, water molecules in the primary hydration spheres of those anions are expected to be depleted in the heavier isotope of oxygen relative to water molecules in bulk, and the degree of the depletion is larger for the chloride ion than for the sulfate ion. Similar tendency was also observed for the isotope preference of hydrogen. No such isotopic preference was observed either for oxygen or for hydrogen in the secondary and outer hydration spheres.

Hydrophilic and Hydrophobic Hydration of Sodium Propanoate and Sodium Butanoate in Aqueous Solution

Aqueous solutions of sodium propanoate (NaOPr) and n-butanoate (NaOBu) have been studied at concentrations of c ~/< 3 M by broadband dielectric relaxation spectroscopy over the frequency range 0.2 ≤ ν/GHz ≤ 89 at 25 °C. Three relaxation modes were resolved, centered at (approximately) 1, 8, and 18 GHz, for both sets of solutions. The two faster modes were assigned to the cooperative relaxation of "slow" and bulk water molecules. Detailed analysis of the spectra indicated that both OPr(-) and OBu(-) were strongly hydrated, with ~23 and ~33 slow water molecules per anion, respectively, at infinite dilution. These effective hydration numbers include ~6 water molecules hydrophilically bound to the carboxylate moiety, with the remainder arising from the hydrophobic hydration of the nonpolar alkyl chains. The latter shows a characteristic rapid decrease with increasing solute concentration, which facilitated the separation of the hydrophobic and hydrophilic contributions. The lowest frequency mode was a composite with contributions from ion-cloud, ion-pair, and anion relaxations. Although this low intensity mode provided specific evidence of weak ion pairing between Na(+)(aq) and the carboxylate anions, reliable estimates of the association constant could not be made because of its composite nature.

Rotational motion of a single water molecule in a buckyball

Encapsulation of a single water molecule in a buckyball (C60) can provide fundamental insights into the properties of water. Investigation of a single water molecule is feasible through its solitary confinement in C60. In this paper, we performed a detailed study of the properties and dynamics of a single water molecule in a buckyball using DFT and MD simulations. We report on the enhancement of rotational diffusion and entropy of a water molecule in C60, compared to a bulk water molecule. H2O@C60 has zero translational diffusion and terahertz revolution frequency. The harmonic, high amplitude rotation of a single water molecule in C60 is compared to stochastic behavior of bulk water molecules. The combination of large rotational and negligible translational motion of water in C60 creates new opportunities in nanotechnology applications.

724 京壁の美観を支える鏝(コテ)の鍛造効果の検証と解明

In previous reports we have found the significant flow differences of kyo-wall compound according to trowel materials with high speed VTR image analysis and the f unction of the old Mizunaze trowel forged by Japanese sword technology inducing peculiar high flow of clay and water compound In this report we have investigated "Noro" water with minute clay exuding from the surface just after applying the earthen compound with the fluid mechanical measurement, kneading test with trowels of every forging stages, the dielectric constant measurement of the surface and bulk water molecules, the X-ray diffraction measurement and the scanning electron microscope. "Noro" exuding mechanism related to the interaction of clay and water molecule which leads to the aesthetic appearance of the Kyo-wall will be reported

Dynamics of Water Inside the Secy Translocon Complex

In bacteria and archea, the insertion of membrane proteins into the plasma membrane is governed by the SecY translocon complex. Understanding how the SecY translocon distinguishes a transmembrane (TM) segment from a secretory one is therefore of the utmost importance. The process of insertion of a TM segment into the membrane resembles a thermodynamic equilibrium process, which has allowed the determination of a “biological” hydrophobicity scale [1,2]. Recent measurements have shown that water-to-membrane partitioning is energetically different from translocon-to-membrane partitioning [3]. A possible explanation is the state of water within the translocon and consequently the strength of the hydrophobic effect. In order to shed light on translocon-to-membrane partitioning, we have investigated water dynamics inside the SecY. We performed molecular dynamics simulations using the crystal structure of SecYE from Pyrococcus furiosus [4] as the initial configuration. Approaching the central region of SecY the hydrogen-bond network between water molecules survives longer than that between bulk water molecules. The rotational motion of water molecules is slowed down and the translational dynamics is characterized by “anomalous” diffusion. These results might explain the difference between translocon-to-membrane partitioning and water-to-membrane partitioning. The features we observed are characteristic of water molecules located close to a macromolecule. Being affected by the complex shape and the physicochemical heterogeneity of the macromolecular surface, these water molecules manifest different properties from those of the bulk phase. A TM helix passing through the SecY protein-conducting channel will feel an environment different from that characterizing bulk water.[1] Hessa et al., Nature, 377, 433 (2005).[2] Hessa et al., Nature, 1026, 450 (2007).[3] K. O-jemalm et al., Proc. Natl. Acad. Sci. USA, E359, 109 (2011).[4] P. F. Egea and R. M. Stroud, Proc. Natl. Acad. Sci. USA, 17182, 107 (2010).

Electronic and Magnetic Changes in a Finite-Sized Single-Walled Zigzag Carbon Nanotube Embedded in Water

In vacuum an open-ended finite-sized zigzag and hydrogen atom terminated carbon nanotube (FS-CNT) has a ground state with antiferromagnetic configuration, and the α and β gaps are degenerated with a magnitude inversely proportional to the nanotube length. However, when a FS-CNT is embedded in a box of water molecules, a single-file hydrogen bonded chain of water molecules (confined water inside) flows through it from one side to the other, while a spatially varying density profile occurs for the bulk water molecules (unconfined water outside). As a consequence, we have observed for an embedded FS-CNT(11,0,L) with L < 2.0 nm important changes in its electronic and magnetic properties. The electronic gap degeneracy is broken, and the gap value for each spin state fluctuates around a mean value which depends on the CNT length. We rationalized these changes by decomposing the fluctuating electric field produced by the water molecules as due to molecules of unconfined water outside and confined water inside the FS-CNT. The confined water inside produces an electric field nearly constant in magnitude and pointing almost along the axial axis of the tube, equivalent to an external uniform electric field with a mean value of 0.56 ± 0.05 V/nm. Meanwhile, the unconfined water outside produces an electric field that fluctuates randomly in direction and magnitude, and it is equivalent to an external uniform electric field with a mean value of 0.7 ± 0.4 V/nm. The maximum electric field observed was 1.7 ± 0.2 V/nm which occurs when both confined water inside and unconfined water outside the electric fields have the same direction. The maximum electric field is three times smaller than the one necessary to change the CNT from semiconductor to half-metallic. The findings are important in devices where solvent molecules change the electronic properties of the CNT.

Structure of the floating water bridge and water in an electric field

The floating water bridge phenomenon is a freestanding rope-shaped connection of pure liquid water, formed under the influence of a high potential difference (approximately 15 kV). Several recent spectroscopic, optical, and neutron scattering studies have suggested that the origin of the bridge is associated with the formation of anisotropic chains of water molecules in the liquid. In this work, high energy X-ray diffraction experiments have been performed on a series of floating water bridges as a function of applied voltage, bridge length, and position within the bridge. The two-dimensional X-ray scattering data showed no direction-dependence, indicating that the bulk water molecules do not exhibit any significant preferred orientation along the electric field. The only structural changes observed were those due to heating, and these effects were found to be the same as for bulk water. These X-ray scattering measurements are supported by molecular dynamics (MD) simulations which were performed under electric fields of 10(6) V/m and 10(9) V/m. Directional structure factor calculations were made from these simulations parallel and perpendicular to the E-field. The 10(6) V/m model showed no significant directional-dependence (anisotropy) in the structure factors. The 10(9) V/m model however, contained molecules aligned by the E-field, and had significant structural anisotropy.

CEST-imaging: A new contrast in MR-mammography by means of chemical exchange saturation transfer

Chemical exchange saturation transfer (CEST) is a technique in H MR imaging (MRI) that enables visualization of chemical exchange processes between protons bound to solutes and surrounding bulk water molecules [1]. To induce a CEST contrast, the off-resonant solute protons are labeled by a saturation radiofrequency (RF) pulse and the label is then transferred to bulk water by chemical exchange. The magnitude of the subsequent reduction of bulk water signal depends consequently on the dynamics of chemical exchange as well as on the ratio of exchangeable solute protons to bulk water protons. The rate constant of chemical exchange (k) is influenced by the pH value and the temperature within the exchange environment. If the latter two parameters can be assumed to be distributed homogeneously in tissue, the CEST effect will be a surrogate marker of the concentration of a certain solute molecule in tissue. In order for a solute molecule to be considered suitable as an endogenous CEST agent, it must carry labile protons that exchange with bulk water at exchange rates that fulfill the condition k <Dw; where Dw is the resonance offset of the solute protons to the water protons in [s]. The most prominent endogenous CEST contrast is amide proton transfer (APT) imaging [2]. It relies on the exchange between amide protons from the backbone of small intracellular mobile proteins or peptides and bulk water. APT imaging has successfully been applied to imaging of ischemic areas in stroke [3], brain tumors [4] and also radiation necrosis [5] due to its strong dependence on tissue pH value. However, of course, aside from its pH sensitivity, APT contrast

Internal structure of water around cations

In the present paper, we use statistical mechanics to probe into the changes induced by cations (Al3+, Mg2+, Ca2+, Li+, Na+, K+, Rb+, Cs+) on the structure of water. The theory aims to find the minimum free energy state, taking into account the hydrogen bonding interactions between water molecules, electrostatic interactions between water and the ion, and thermal energy. Water molecules in the first shell of Na+ ions are found to largely retain their structure; the average number of H-bonds (<nHB>) and the average dipolar alignment (<θ>) of a water molecule are only marginally different from the corresponding values of bulk water. This is made possible by the “caging” of the Na+ ions by water molecules. The magnitudes of <nHB> and <θ> are, however, found to decrease for ions on either side of Na+ ions in the Hofmeister Series. Water molecules around small ions with high charge density (e.g. Al3+) are found to strongly align their dipoles in the direction of field, despite the reduction in the number of H-bonds per molecule. Those around large ions with low charge density (e.g. Cs+) are oriented such that one of their H-bond axes involving a lone pair of electrons is directly facing the ion, thereby maximizing their H-bond interactions at the other three bonding sites. Beyond the first shell of all the ions studied, the degree of hydrogen bonding is similar to that of bulk water molecules. Changes in the molecular orientation and non-linear polarization effects, however, persist up to ~3–4 hydration shells in the case of salting-in ions, and ~7–9 shells in the case of salting-out ions.

An Internal Water-Retention Site in the Rhomboid Intramembrane Protease GlpG Ensures Catalytic Efficiency

Rhomboid proteases regulate key cellular pathways, but their biochemical mechanism including how water is made available to the membrane-immersed active site remains ambiguous. We performed four prolonged molecular dynamics simulations initiated from both gate-open and gate-closed states of Escherichia coli rhomboid GlpG in a phospholipid bilayer. GlpG was notably stable in both gating states, experiencing similar tilt and local membrane thinning, with no observable gating transitions, highlighting that gating is rate-limiting. Analysis of dynamics revealed rapid loss of crystallographic waters from the active site, but retention of a water cluster within a site formed by His141, Ser181, Ser185, and/or Gln189. Experimental interrogation of 14 engineered mutants revealed an essential role for at least Gln189 and Ser185 in catalysis with no effect on structural stability. Our studies indicate that spontaneous water supply to the intramembrane active site of rhomboid proteases is rare, but its availability for catalysis is ensured by an unanticipated active site element, the water-retention site.

Intramolecular vibrational coupling in water molecules revealed by compatible multiple nonlinear vibrational spectroscopic measurements

The complex structure of water and its interactions with solid surfaces require the development of multiple vibrational spectroscopic measurements to study the molecular structure of interfacial water and bulk water near the solid surface. In this study, a newly developed compatible multiple nonlinear vibrational spectroscopy system has been applied to investigate the molecular structure of water in the interfacial region of an ionic solid (CaF(2) substrate) and bulk isotopic D(2)O-HOD-H(2)O mixtures. Using this compatible system, the sum frequency generation (SFG) vibrational spectra and infrared-infrared-visible three-pump-field four-wave-mixing (IIV-TPF-FWM) spectra of the same water molecules can be collected at the same experimental geometry. It is found that SFG and IIV-TPF-FWM can be used to characterize the molecular structures of interfacial water and bulk water molecules at an interfacial distance below 42 nm, respectively. SFG and IIV-TPF-FWM results both suggest an intramolecular vibrational coupling dominates the spectra. The results achieved by this method are helpful to clarify the origination of the vibrational coupling of the interfacial water as well as the bulk water near the solid surface.

A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale systems that require massively parallel computers. The IPS method has two different versions: IPSn and IPSp. The basic idea is the same expect for the fact that the IPSn method is applied to calculations for point charges, while the IPSp method is used to calculate polar molecules. The concept of the IPS/Tree method is available for both IPSn and IPSp as IPSn/Tree and IPSp/Tree. Even though the accuracy of the Coulomb forces with tree-based method is well known, the accuracy for the combination of the IPS and tree-based methods is unclear. Therefore, in order to evaluate the accuracy of the IPS/Tree method, we performed molecular dynamics simulations for 32,000 bulk water molecules, which contains around 10(5) point charges. IPSn/Tree and IPSp/Tree were both applied to study the interaction calculations of Coulombic forces. The accuracy of the Coulombic forces and other physical properties of bulk water systems were evaluated. The IPSp/Tree method not only has reasonably small error in estimating Coulombic forces but the error was almost the same as the theoretical error of the ordinary tree-based method. These facts show that the algorithm of the tree-based method can be successfully applied to the IPSp method. On the other hand, the IPSn/Tree has a relatively large error, which seems to have been derived from the interaction treatment of the original IPSn method. The self-diffusion and radial distribution functions of water were calculated each by both the IPSn/Tree and IPSp/Tree methods, where both methods showed reasonable agreement with the Ewald method. In conclusion, the IPSp/Tree method is a potentially fast and sufficiently accurate technique for predicting transport coefficients and liquid structures of water in a homogeneous system.

Water Dynamics at Interfaces and Solutes: Disentangling Free Energy and Diffusivity Contributions

The dynamics of single water molecules in bulk and at interfaces is studied by means of molecular dynamics simulations. We use a recently developed stochastic method based on the Fokker-Planck equation to disentangle the contributions of the free energy and diffusivity profiles on the local dynamics. The strong variations found in the diffusivity profiles are crucial for accurately modeling the water kinetics. A comparison of hydrophobic and hydrophilic substrates and solutes yields significant differences in the diffusivities, which can be attributed to the presence of hydrogen bonds.

18O/16O and D/H Isotopic Preference in Hydration Spheres of Alkali Metal Ions

Abstract With the final goal set at theoretical elucidation of experimentally observed isotope salt effects, molecular orbital calculations were performed to estimate the 18O/16O and D/H isotopic reduced partition function ratios (RPFRs) of water molecules around lithium, sodium, and potassium ions. As model water molecules in the ith hydration sphere of the cation in aqueous solutions containing that cation, we considered water molecules in the ith hydration sphere that were surrounded by water molecules in the (i+1)th hydration sphere in clusters, M+(H2O)n (M = Li, Na or K; n up to 100). The calculations indicated that the decreasing order of the 18 O preference over 16 O in the primary hydration sphere is: Li+ &gt; (bulk water) ≥ Na+ &gt; K+. That is, water molecules in the primary hydration spheres of the Li+, Na+, and K+ ions are, respectively, enriched, slightly depleted, and depleted in the heavier isotope of oxygen relative to water molecules in bulk. No such preference was observed for hydrogen isotopes in any hydration sphere or for oxygen isotopes in the secondary and outer hydration spheres.

Quantitative separation of CEST effect from magnetization transfer and spillover effects by Lorentzian-line-fit analysis of z-spectra

Chemical exchange saturation transfer (CEST) processes in aqueous systems are quantified by evaluation of z-spectra, which are obtained by acquisition of the water proton signal after selective RF presaturation at different frequencies. When saturation experiments are performed in vivo, three effects are contributing: CEST, direct water saturation (spillover), and magnetization transfer (MT) mediated by protons bound to macromolecules and bulk water molecules. To analyze the combined saturation a new analytical model is introduced which is based on the weak-saturation-pulse (WSP) approximation. The model combines three single WSP approaches to a general model function. Simulations demonstrated the benefits and constraints of the model, in particular the capability of the model to reproduce the ideal proton transfer rate (PTR) and the conventional MT rate for moderate spillover effects (up to 50% direct saturation at CEST-resonant irradiation). The method offers access to PTR from z-spectra data without further knowledge of the system, but requires precise measurements with dense saturation frequency sampling of z-spectra. PTR is related to physical parameters such as concentration, transfer rates and thereby pH or temperature of tissue, using either exogenous contrast agents (PARACEST, DIACEST) or endogenous agents such as amide protons and –OH protons of small metabolites.

A Quantitative Perspective on Hydrophobic Interactions in the Gas-Phase

Mass spectrometry has become a powerful tool for determining the composition, stoichiometry, subunit interactions, and architectural organization of non-covalent protein complexes. The vast majority of assemblies studied so far by this approach are those that contain a sufficient amount of electrostatic interactions and hydrogen bonds that can survive the transition from solution to the gas-phase and maintain the structural features of the vaporized ions. An intriguing question that naturally arises is whether mass spectrometry can also be harnessed for the study of molecular systems dominated by non-polar interactions. Here we address this issue and discuss the fate of hydrophobic complexes in the absence of bulk water molecules. We emphasize the progress that has been accomplished in this field that is moving towards the analysis of larger and more complex hydrophobic systems. We attribute this advance to recent developments of mass spectrometry and its application to non-covalent complexes in general, and to the understanding of experimental and biochemical conditions for the preservation of hydrophobic interactions in particular. Furthermore, we discuss the ability of mass spectrometry to serve as a quantitative tool for assessing the strength, binding energies, and stoichiometries of hydrophobic interactions. Overall, we aim to stimulate research in this area and to establish mass spectrometry as a tool for analyzing hydrophobic interactions within complex biological systems.

Dependence of the number of hydrogen bonds per water molecule on its distance to a hydrophobic surface and a thereupon-based model for hydrophobic attraction

A water molecule in the vicinity of a hydrophobic surface forms fewer hydrogen bonds than a bulk molecule because the surface restricts the space available for other water molecules necessary for its hydrogen-bonding. In this vicinity, the number of hydrogen bonds per water molecule depends on its distance to the surface. Considering the number of hydrogen bonds per bulk water molecule (available experimentally) as the only reference quantity, we propose an improved probabilistic approach to water hydrogen-bonding that allows one to obtain an analytic expression for this dependence. (The original version of this approach [Y. S. Djikaev and E. Ruckenstein, J. Chem. Phys. 130, 124713 (2009)] provides the number of hydrogen bonds per water molecule in the vicinity of a hydrophobic surface as an average over all possible locations and orientations of the molecule.) This function (the number of hydrogen bonds per water molecule versus its distance to a hydrophobic surface) can be used to develop analytic models for the effect of hydrogen-bonding on the hydration of hydrophobic particles and their solvent-mediated interaction. Presenting a model for the latter, we also examine the temperature effect on the solvent-mediated interaction of two parallel hydrophobic plates.