Neighboring Water Molecules Research Articles

Cooperativity in Ordinary Ice and Breaking of Hydrogen Bonds

The total interaction energy between two H-bonded water molecules in a condensed phase is composed of a binding energy between them and an energy due to a cooperative effect. An approximate simple expression is suggested for the dependence of the interaction energy between two H-bonded water molecules on the number of neighboring water molecules with which they are H-bonded. Using this expression, the probabilities of breaking a H bond with various numbers of H-bonded neighbors are estimated. These probabilities are used in computer simulations of the breaking of specified fractions of H bonds in an ordinary (hexagonal) ice. A large "piece" of hexagonal ice (up to 8 millions molecules) is built up, and various percentages of H bonds are considered broken. It is shown that 62-63% of H bonds must be broken in order to disintegrate the "piece" of ice into disconnected clusters. This value is only a little larger than the percolation threshold (61%) predicted both by the percolation theory for tetrahedral ice and by simulations in which all H bonds were considered equally probable to be broken. When the percentage of broken bonds is smaller than 62-63%, there is a network of H-bonded molecules which contains the overwhelming majority of water molecules. This result contradicts some models of water which consider that water consists of a mixture of water clusters of various sizes. The distribution of water molecules with unequal probabilities for breaking is compared with the simulation involving equal probabilities for breaking. It was found that in the former case, there is an enhanced number of water monomers without H bonds, that the numbers of 2- and 3-bonded molecules are smaller, and the number of 4-bonded molecules is larger than in the latter case.

Energetics of ice nanotubes and their encapsulation in carbon nanotubes from density-functional theory

We have performed total-energy electronic-structure calculations based on the density-functional theory that clarify atomic and electronic structures of ice nanotubes encapsulated in carbon nanotubes. We have found that three tubular structures of ice are stable in carbon nanotubes. The structural characteristics of these ice nanotubes is a straight stacking or helical arrangement of polygonal units consisting of water molecules. In these stable ice nanotubes, each water molecule is fourfold coordinated with neighboring water molecules through hydrogen bonds. The energy gain upon encapsulation of ice nanotubes in carbon nanotubes is found to be an order of $10\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$ per water molecule, whereas the energy gain to form ice nanotubes from isolated water molecules is about a half eV per molecule. Carbon nanotubes act as a template to form the new polymorph of ice. Detailed structural analysis has revealed a role of hydrogen-bond angles in determining energetics of the ice nanotubes. We have also clarified that energy gaps of ice nanotubes are comparable with the gap of the most stable ice polymorph Ih and that the electronic structure of ice nanotubes encapsulated in carbon nanotubes is a superposition of the energy bands of the constituents.

Ionization of sodium in water clusters

Structures of Na(H2O)n and Na+(H2O)n clusters with n = 1−6, 19, and 28 are determined in the second order of the Moller-Plesset perturbation theory with the use of extended atomic basis set 6–31++G**. It is found that when the number of molecules is sufficient for the formation of two solvation shells around sodium, a continuous hydrogen-bond network is formed in both neutral and charged clusters, and the orientation of each molecule is determined by the balance between interactions with the neighboring water molecules and with the field of the central particle. In the cations, this field is stronger, and up to the third solvation shell, molecules have a predominant orientation with respect to sodium. In the neutral clusters, with an increase in the number of water molecules, the maximum of the electron density distribution of the highest occupied molecular orbital becomes more distant from the sodium nucleus, being shifted toward the cluster surface. The energy of this orbital accordingly decreases in absolute value approaching 22 kcal/mol inmicroparticles. In the charged clusters, the distribution of the positive charge generally correlates with the character of the highest occupied orbital in the neutral systems, so that with an increase in the number of molecules, the atomic charge of sodium decreases and tends to zero as n → ∞. The ionization potential of sodium changes in inverse proportion to the linear size of the cluster, and should not exceed 1.1 eV in watermicroparticles.

Interactions between Phosphate and Water in Solution: A Natural Bond Orbital Based Analysis in a QM/MM Framework

The natural bond orbital (NBO) and natural energy decomposition analysis (NEDA) calculations are used to analyze the interaction between mono-methyl phosphate-ester (MMP) and its solvation environment in a combined quantum mechanical/molecular mechanical (QM/MM) framework. The solute-solvent configurations are generated using a specific parametrization of the self-consistent-charge density functional tight-binding (SCC-DFTB) model for the MMP and TIP3P for water. The NBO and NEDA calculations are done with several QM/MM partitioning schemes with HF/6-31+G** as the QM level. Regardless of the size of the QM region, a notable amount of charge transfer is observed between MMP and the neighboring water molecules and the charge-transfer interactions are, in the NEDA framework, as important as the electric (electrostatic and polarization) components. This work illustrates that NBO based analyses are effective tools for probing intermolecular interactions in condensed phase systems.

Electrostatic gating of a nanometer water channel

Water permeation across a single-walled carbon nanotube (SWNT) under the influence of a mobile external charge has been studied with molecular dynamics simulations. This designed nanopore shows an excellent on-off gating behavior by a single external charge (of value +1.0e): it is both sensitive to the available charge signal when it is close (less than a critical distance of 0.85 A or about half the size of a water molecule) and effectively resistant to charge noise, i.e., the effect on the flow and net flux across the channel is found to be negligible when the charge is >0.85 A away from the wall of the nanopore. This critical distance can be estimated from the interaction balance for the water molecule in the SWNT closest to the imposed charge with its neighboring water molecules and with the charge. The flow and net flux decay exponentially with respect to the difference between these two interaction energies when the charge gets closer to the wall of the SWNT and reaches a very small value once the charge crosses the wall, suggesting a dominating effect on the permeation properties from local water molecules near the external charge. These findings might have biological implications because membrane water channels share a similar single-file water chain inside these nanoscale channels.

Evidence for Water Rings in the Hexahydrated Sulfate Dianion from IR Spectroscopy

Whereas isolated SO42- is unstable, hydrated clusters of this dianion have been formed and investigated using a variety of different methods. Several structures of [SO4(H2O)6]2- have been proposed that account for its high stability in the gas phase. Zhou et al. [J. Chem. Phys. 2006, 125, 111102] recently reported infrared spectra of [SO4(H2O)n]2- in the 540−1850 cm-1 region and assigned the spectrum of the hexahydrated ion to a Td symmetry structure in which all six water molecules donate two hydrogen bonds to the sulfate core. Here, an infrared spectrum of this ion in the hydrogen stretch region (2620−3840 cm-1) and B3LYP/AUG-cc-pVDZ calculations indicate that a significant population of these ions correspond to lower symmetry structures containing water rings in which each water molecule donates hydrogen bonds to both the sulfate dianion and a neighboring water molecule. These calculations indicate that inter-water hydrogen bonds are slightly favored over additional solvation of the dianion core. These results demonstrate that the low- and high-frequency infrared spectra of this ion provide complementary information, and the combination can greatly enhance structural elucidation of these hydrated ions.

Supramolecular self-assembly of dihydroxy tin(iv) porphyrin stabilized helical water chains

The supramolecular assembly formed in the solid-state by the interaction of dihydroxy tin(IV) tetra(4-pyridyl)porphyrin (TPyP) with water is discussed. The resulting pseudo two-dimensional array of water molecules are ordered into helical chains by hydrogen bonding between neighboring water molecules along the chain as well as hydrogen bonding between water molecules and the axial hydroxyl and pyridyl groups of the tin(IV) porphyrin.

Hydrogen Bonding of Water Confined in Controlled-Pore Glass 10-75 Studied by ¹H-Solid State NMR

In this paper a possible explanation for an unexpected ortho/para-water ratio in the gas clouds of comets is given. The description is based on the quantum-mechanical density matrix formalism and the spin temperature concept. Only the nuclear spin system is treated quantum-mechanically. Employing the model of a four spin system, created by two nearest neighbour water molecules, spin eigenstates and their dynamics under the influence of their mutual dipolar interactions are studied. It is shown that a fast conversion between ortho- and para-states occurs on a msec time scale, caused by the intermolecular homonuclear magnetic dipolar interaction. Moreover the spin eigenstates of water in an ice crystal are determined by magnetic dipolar interactions and are not given by normal ortho- and para-H₂O states of gaseous water. As a result of this the spin temperature of gaseous water evaporated from ice depends strongly on its evaporation history and the ortho/para-ratio of water molecules are only an indirect measure of the temperature of ice crystals from where they descend. This result could explain the unexpected experimentally observed ortho/para-ratios in the clouds of comets.

Conformational Coupling between the Cytoplasmic Carboxylic Acid and the Retinal in a Fungal Light-Driven Proton Pump

Many fungal rhodopsins, eukaryotic structural homologues of the archaeal light-driven proton pump bacteriorhodopsin, have been discovered in the course of genome sequencing projects. Recently, two fungal rhodopsins were characterized in vitro and exhibited very different photochemical behavior. Neurospora rhodopsin possesses a slow photocycle and shows no ion transport, reminiscent of sensory rhodopsins, while Leptosphaeria rhodopsin has a fast bacteriorhodopsin-like photocycle and pumps protons light-dependently. Such a dramatic difference is surprising considering the very high degree of sequence homology of the two proteins. In this paper, we investigate whether the chemical structure of a cytoplasmic carboxylic acid, the homologue of Asp-96 of bacteriorhodopsin serving as a proton donor for the retinal Schiff base, can define the photochemical properties of fungal rhodopsins. We studied mutants of Leptosphaeria rhodopsin in which this aspartic acid was replaced with Glu or Asn using spectroscopy in the infrared and visible ranges. We show that Glu at this position is inefficient as a proton donor similar to a nonprotonatable Asn. Moreover, this replacement induces long-range structural perturbations of the retinal environment, as evidenced by changes in the vibrational bands of retinal (especially, hydrogen-out-of-plane modes) and neighboring aspartic acids and water molecules. The conformational coupling of the mutation site to the retinal may be mediated by helical rearrangements as suggested by the changes in amide and proline vibrational bands. We conclude that the difference in the photochemical behavior of fungal rhodopsins from Leptosphaeria and Neurospora may be ascribed, to some extent, to the replacement of the cytoplasmic proton donor Asp with Glu.

The role of water in the initial steps of methanol oxidation on Pt(2 1 1)

We report results of quantum-chemical calculations within the framework of density functional theory for the oxidation of methanol on the (2 1 1) face of a platinum single crystal. Similar to the reaction pathway on the low indexed (1 1 1) crystal face water plays an important role as found from energy minimization calculations: the adsorption of methanol on charged and uncharged surfaces is strongly enhanced by the formation of a hydrogen bond to a coadsorbed water molecule. The methanol is adsorbed via a methyl hydrogen atom preceding scission of one of the CH-bonds as the first reaction step. In the presence of additional water, e.g., from a liquid phase, the onset of the oxidation reaction is favored by a coadsorbed neighboring water molecule which forms a hydrogen bond with the methanol OH-group. At a minimum number of adjacent water molecules ( n ≥ 2 ) the CH-bond as well as the OH-bond are cleaved on charged surfaces. The protonic charge stemming from the dissociation of the methanol hydroxyl group is delocalized inside the aqueous cluster and formaldehyde is formed as an intermediate product.

Ab initio QM/MM dynamics of H3O+ in water

A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6-8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O4+) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O2+) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton.

Oxidative Damage to DNA: Counterion-Assisted Addition of Water to Ionized DNA

Oxidative damage to DNA, implicated in mutagenesis, aging, and cancer, follows electron loss that generates a radical cation that migrates to a guanine, where it may react with water to form 8-oxo-7,8-dihydroguanine (8-OxoG). Molecular dynamics and ab initio quantum simulations on a B-DNA tetradecamer reveal activated reaction pathways that depend on the local counterion arrangement. The lowest activation barrier, 0.73 eV, is found for a reaction that starts from a configuration where a Na(+) resides in the major groove near the N7 atoms of adjacent guanines, and evolves through a transition state where a bond between a water oxygen atom and a carbon atom forms concurrently with displacement of a proton toward a neighboring water molecule. Subsequently, a bonded complex of a hydronium ion and the nearest backbone phosphate group forms. This counterion-assisted proton shuttle mechanism is supported by experiments exploiting selective substitution of backbone phosphates by methylphosphonates.

Investigations of the hydrophobic and hydrophilic interactions in polymer–water systems by ATR FTIR and Raman spectroscopy

ATR FTIR and Raman spectra of polymers containing amide groups in the main chain and in the side chain and of the amide low-molecular-weight model compounds in water media were measured. The hydrophobic and hydrophilic interactions of the dissolved compounds with the neighboring water molecules are reflected in the wavenumbers of the CH 3 stretching and of the Amide I and II vibrations. The possibility of the existence of β-sheet-like structures in polypeptides surrounded by water molecules is also discussed.

Protons colliding with ice: Bouncing, sticking, splashing

Results of classical trajectory calculations on the sticking of H + to the basal plane (0 0 0 1) face of crystalline ice, at a surface temperature of 80 K are presented. The calculations were performed for incidence energies ranging from 0.1 to 4.0 eV, for normal and off-normal incidence. Significant reflection is predicted at low incidence energies and large incidence angles. This reflection is due to repulsive electrostatic interactions between the incident proton and the positively charged upward pointing H-atoms of the surface water molecules. The sticking probability converges to 1 for incidence energies ⩾0.8 eV, for all values of incidence angles considered here. The strong interaction with the neighbouring water molecules leads to a local rupture of the hydrogen bonding network, resulting in collision induced desorption of water (puffing), a process that occurs with significant probability even at the lowest incidence energy considered. The water desorption probability is found to be independent on the angle of incidence, but increases with the incidence energy. In nearly all trajectories in which water desorption occurs, a single water molecule is desorbed from the topmost monolayer. In nearly all sticking trajectories, the proton is implanted into the ice surface, with a penetration depth that increases with the incidence energy, and decreases with the angle of incidence for high incidence energies.

Three Structural Roles for Water in Bone Observed by Solid-State NMR

Hydrogen-bearing species in the bone mineral environment were investigated using solid-state NMR spectroscopy of powdered bone, deproteinated bone, and B-type carbonated apatite. Using magic-angle spinning and cross-polarization techniques three types of structurally-bound water were observed in these materials. Two of these water types occupy vacancies within the apatitic mineral crystal in synthetic carbonated apatite and deproteinated bone and serve to stabilize these defect-containing crystals. The third water was observed at the mineral surface in unmodified bone but not in deproteinated bone, suggesting a role for this water in mediating mineral-organic matrix interactions. Direct evidence of monohydrogen phosphate in a 1H NMR spectrum of unmodified bone is presented for the first time. We obtained clear evidence for the presence of hydroxide ion in deproteinated bone by 1H MAS NMR. A 1H-31P heteronuclear correlation experiment provided unambiguous evidence for hydroxide ion in unmodified bone as well. Hydroxide ion in both unmodified and deproteinated bone mineral was found to participate in hydrogen bonding with neighboring water molecules and ions. In unmodified bone mineral hydroxide ion was found, through a 1H-31P heteronuclear correlation experiment, to be confined to a small portion of the mineral crystal, probably the internal portion.

Monte Carlo Simulations of the Hydrophobic Effect in Aqueous Electrolyte Solutions

The hydrophobic interaction between two methane molecules in salt-free and high salt-containing aqueous solutions and the structure in such solutions have been investigated using an atomistic model solved by Monte Carlo simulations. Monovalent salt representing NaCl and divalent salt with the same nonelectrostatic properties as the monovalent salt have been used to examine the influence of the valence of the salt species. In salt-free solution the effective interaction between the two methane molecules displayed a global minimum at close contact of the two methane molecules and a solvent-separated secondary minimum. In 3 and 5 M monovalent salt solution the potential of mean force became slightly more attractive, and in a 3 M divalent salt solution the attraction became considerably stronger. The structure of the aqueous solutions was determined by radial distribution functions and angular probability functions. The distortion of the native water structure increased with ion valence. The increase of the hydrophobic attraction was associated with (i) a breakdown of the tetrahedral structure formed by neighboring water molecules and of the hydrogen bonds between them and (i) the concomitant increase of the solution density.

QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

Stretching of hydrogen-bonded OH in the lowest singlet excited electronic state of water dimer

The lowest singlet excited electronic state of water monomer in the gas phase is strictly dissociative along a OH stretch coordinate but changes its nature when the stretched OH moiety is hydrogen bonded to a neighboring water molecule. This work extends previous exploration of the water dimer excited singlet potential-energy surface, using computational methods that are reliable even at geometries well removed from the ground-state equilibrium. First, the hydrogen-bonded OH moiety is stretched far enough to establish the existence of a barrier that is sufficient to support a quasibound vibrational state of the OH oscillator near the Franck-Condon region. Second, the constraint of an icelike structure is relaxed, and it is found that a substantial fraction of liquidlike structures also supports a quasibound vibrational state. These potential-energy explorations on stretching of the hydrogen-bonded OH moiety in a water dimer are discussed as a model for understanding the initial dynamics upon excitation into the lowest excited singlet state of condensed water. The possibility is raised that the excited-state lifetime may be long enough to allow for exciton migration, which would provide a mechanism for energy transport in condensed water phases.

Structural Correlations and Motifs in Liquid Water at Selected Temperatures: Ab Initio and Empirical Model Predictions

To gain further insight into liquid water's structure and explore the role of different physical forces underlying the interaction between water molecules, the radial and angular structure of water is probed as a function of temperature for a carefully selected set of theoretical models. Simulations are performed with empirical rigid, empirical polarizable, empirical flexible with classical and quantum nuclei, and ab initio models with classical nuclei at 300 and 353 K and quantum nuclei at 300 K. The predicted radial distribution functions, spatial maps, and angular distributions of the neighboring water molecules are consistent with a model of liquid water in which water molecules are tetrahedrally coordinated. In addition, three-dimensional joint distribution functions are introduced and analyzed. By comparison of the functions obtained for hexagonal ice to those of liquid water, several thermally disordered, ice-like cluster structures are identified in the fluid.

Hydroxyl Radical and Hydroxide Ion in Liquid Water: A Comparative Electron Density Functional Theory Study

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.