Tetrahedral Hydrogen Bond Research Articles

Hydrogen bonded networks in supercritical water.

In this study, the structure of supercritical water (SCW) is investigated by Raman spectroscopy and molecular dynamics simulations. It was found that the hydrogen bonding in water is closely related to temperature and pressure (or water density). According to the Raman spectroscopic study of SCW, the existence of tetrahedral hydrogen bonds in SCW is also affected by the density of SCW. In addition, for SCW with critical density (0.322 g cm(-3)), we suggest that the tetrahedral hydrogen bonding is absent at water critical point (647 K and 22.1 MPa) based on Raman evidence. From the dependence of νmax of the Raman OH stretching bands on temperature and pressure, the structure of SCW can be divided into three-dimensional and chain (or string) hydrogen bonded networks, which correspond to liquid- and gas-like phases, respectively.

Effects of hydrophobic hydration on polymer chains immersed in supercooled water

A multiscale simulation of a hydrophobic polymer chain immersed in water including the supercooled region is presented. Solvent effects on the polymer conformation were taken into account via liquid–state density functional theory in which a free-energy functional model was constructed using a density response function of bulk water, determined from a molecular dynamics (MD) simulation. This approach overcomes sampling problems in simulations of high-viscosity polymer solutions in the deeply supercooled region. Isobars determined from the MD simulations of 4000 water molecules suggest a liquid–liquid transition in the deeply supercooled region. The multiscale simulation reveals that a hydrophobic polymer chain exhibits swelling upon cooling along isobars below a hypothesized second critical pressure; no remarkable swelling is observed at higher pressures. These observations agree with the behavior of a polymer chain in a Jagla solvent model that qualitatively reproduces the thermodynamics and dynamics of liquid water. A theoretical analysis of the results obtained from the multiscale simulation show that a decrease in entropy due to the swelling arises from the formation of a tetrahedral hydrogen bond network in the hydration shell.

Dielectric and structural properties of aqueous nonpolar solute mixtures

The dielectric properties and molecular structure of water mixtures with different nonpolar solutes (methane and noble gases) are studied using molecular dynamics. The water-water, water-solute, and solute-solute interactions are calculated using the combination of a polarizable potential [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] for water plus the Lennard-Jones potential. The effect of solute size and concentration on the solubility of the system, hydrogen bonding, dielectric constant, and dipole moment are investigated over a temperature range of 278-750 K and solute percentage mole fractions up to 30%. Solute particles affect the structure of water, resulting in the compression of oxygen-oxygen and oxygen-hydrogen radial distribution functions. The influence of the solute extends both to relatively low concentrations and high temperatures. The coordination numbers of aqueous solutions of the nonpolar solutes appear to be proportional to the size of the solute particles. Our study shows the destructive influence of the nonpolar solute on both the tetrahedral water structure and hydrogen bond formation at solute concentrations greater than 30%. The presence of nonpolar particles typically decreases both the dielectric constant and dipole moment. The decrease of dielectric constant and water dipole moment is directly proportional to the solute concentration and temperature.

Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models.

Water is one of the simplest molecules in existence, but also one of the most important in biological and engineered systems. However, understanding the structure and dynamics of liquid water remains a major scientific challenge. Molecular dynamics simulations of liquid water were performed using the water models TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP to calculate the radial distribution functions (RDFs), the relative angular distributions, and the excess enthalpies, entropies, and free energies. In addition, lower-order approximations to the entropy were considered, identifying the fourth-order approximation as an excellent estimate of the full entropy. The second-order and third-order approximations are ~20% larger and smaller than the true entropy, respectively. All four models perform very well in predicting the radial distribution functions, with the TIP5P-Ewald model providing the best match to the experimental data. The models also perform well in predicting the excess entropy, enthalpy, and free energy of liquid water. The TIP4P-2005 and SWM4-NDP models are more accurate than the TIP3P-Ewald and TIP5P-Ewald models in this respect. However, the relative angular distribution functions of the four water models reveal notable differences. The TIP5P-Ewald model demonstrates an increased preference for water molecules to act both as tetrahedral hydrogen bond donors and acceptors, whereas the SWM4-NDP model demonstrates an increased preference for water molecules to act as planar hydrogen bond acceptors. These differences are not uncovered by analysis of the RDFs or the commonly employed tetrahedral order parameter. However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy.

Computer simulations of dynamic crossover phenomena in nanoconfined water **Dedicated to Professor Sow-Hsin Chen on the occasion of his 75th birthday.

In order to study dynamic crossover phenomena in nanoconfined water we performed a series of molecular dynamics (MD) computer simulations of water clusters adsorbed in zeolites, which are microporous crystalline aluminosilicates containing channels and cavities of nanometric dimensions. We used a sophisticated empirical potential for water, including the full flexibility of the molecule and the correct response to the electric field generated by the cations and by the charged atoms of the aluminosilicate framework. In addition, the full flexibility of the aluminosilicate framework was included in the calculations. Previously reported and new simulations of water confined in a number of different types of zeolites in the temperature range 100–300 K and at various coverage are discussed in connection with the experimental data. Dynamic crossover phenomena are found in all the considered cases, in spite of the different shape and size of the clusters, even when the confinement hinders the formation of tetrahedral hydrogen bonds for water molecules. Hypotheses about the possible dynamic crossover mechanisms are proposed.

Depolarization of water in protic ionic liquids

A mixture of the protic ionic liquid mono-methylammonium nitrate with 1.6 wt% water was investigated from Car-Parrinello molecular dynamics simulations. In contrast to imidazolium-based ionic liquids, the cation possesses strong directional hydrogen bonds to water and all hydrogen bonds in the mixture have a comparable strength. This results in a good incorporation of water into the hydrogen bond network of mono-methylammonium nitrate and a tetrahedral hydrogen bond coordination of water. Hence, one might expect a larger dipole moment of water in the investigated mixture compared to neat water due to the good hydrogen bond network incorporation and the charged vicinity of water in the protic ionic liquid. However, the opposite is observed pointing to strong electrostatic screening in protic ionic liquids. Additionally, the influence of water on the properties of the protic ionic liquid is discussed.

Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: A Raman scattering and molecular dynamics simulation study

The low-frequency (omega<400 cm(-1)) vibrational properties of lysozyme in aqueous solutions of three well-known protecting sugars, namely, trehalose, maltose, and sucrose, have been investigated by means of complementary Raman scattering experiments and molecular dynamics simulations. The comparison of the Raman susceptibility chi(")(omega) of lysozyme/water and lysozyme/sugar/water solutions at a concentration of 40 wt % with the chi(") of dry lysozyme suggests that the protein dynamics mostly appears in the broad peak around 60-80 cm(-1) that reflects the vibrations experienced by atoms within the cage formed by their neighbors, whereas the broad shoulder around 170 cm(-1) mainly stems from the intermolecular O-H...O stretching vibrations of water. The addition of sugars essentially induces a significant high frequency shift and intensity reduction of this band that reveal a slowing down of water dynamics and a distortion of the tetrahedral hydrogen bond network of water, respectively. Furthermore, the lysozyme vibrational densities of states (VDOS) have been determined from simulations of lysozyme in 37-60 wt % disaccharide aqueous solutions. They exhibit an additional broad peak around 290 cm(-1), in line with the VDOS of globular proteins obtained in neutron scattering experiments. The influence of sugars on the computed VDOS mostly appears on the first peak as a slight high-frequency shift and intensity reduction in the low-frequency range (omega<50 cm(-1)), which increase with the sugar concentration and with the exposition of protein residues to the solvent. These results suggest that sugars stiffen the environment experienced by lysozyme atoms, thereby counteracting the softening of protein vibrational modes upon denaturation, observed at high temperature in the Raman susceptibility of the lysozyme/water solution and in the computed VDOS of unfolded lysozyme in water. Finally, the Raman susceptibility of sugar/water solutions and the calculated VDOS of water in the different lysozyme solutions confirm that sugars induce a significant strengthening of the hydrogen bond network of water that may stabilize proteins at high temperatures.

Universality of Separation Behavior of Relaxation Processes in Supercooled Aqueous Solutions As Revealed by Broadband Dielectric Measurements

We investigate the universality of the relaxation processes for high-water-content aqueous solutions in a supercooled and glassy state, to clarify the molecular dynamics of water in aqueous solutions. The appearance of the additional process at the crossover temperature is due to structured water arising, and it is a universal feature of aqueous solutions. The normalized relaxation strength of the beta process plotted against reciprocal temperature obeys -3 power law that is due the arrangement region of the water molecules through the tetrahedral hydrogen bond structure.

Investigation of Hydration Structures of Proteins

Water is a mother liquid of life. To understand why water is indispensable to life, I have been investigating the structures and interactions at protein-water interface, i.e. the hydration structures of proteins, by cryogenic X-ray crystallography and molecular dynamics simulation. Through developing devices and experimental techniques in cryogenic X-ray diffraction experiments, I realized that cryogenic X-ray crystallography is one of techniques effectively observe hydration structures of proteins surface. In addition, the author developed a novel calculation codes to characterize systematically hydration structures of the protein structures determined at around 100 K, as to the amount of water molecules, the hydrogen-bond geometries, the local and the global distribution of them on the surface of proteins. The standard tetrahedral hydrogen bonds of water molecules in bulk water were retained in the hydration structures and contributed to extend three-dimensional network of hydrogen bonds among hydration water molecules and oxygen and nitrogen atoms of protein surface. In cryo-crystallography of multi-subunit or multi-domain proteins, the reorganization of hydration structure occurred with the dynamical motions of proteins. In that, water molecules act as inhibitors for protein motions, glue to stabilize the higher-order structures or lubricant to realize conformational changes by utilizing its tetrahedral arms of hydrogen bonds. Thus, hydration water molecules must have great influences on the dynamics and functions of proteins in aqueous solution.

Metabasin dynamics and local structure in supercooled water

We employ the distance matrix method to investigate metabasin dynamics in supercooled water. We find that the motion of the system consists in the exploration of a finite region of configuration space (enclosing several distinct local minima), named metabasin, followed by a sharp crossing to a different metabasin. The characteristic time between metabasin transitions is comparable to the structural relaxation time, suggesting that these transitions are relevant for the long-time dynamics. The crossing between metabasins is accompanied by very rapid diffusional jumps of several groups of dynamically correlated particles. These particles form relatively compact clusters and act as cooperative relaxing units responsible for the density relaxation. We find that these mobile particles are often characterized by an average coordination larger than four, i.e., they are located in regions where the tetrahedral hydrogen bond network is distorted.

Water-protein interactions from high-resolution protein crystallography.

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein-water interface have been investigated by cryogenic X-ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen-bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three-dimensional chain connection of a hydrogen-bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico-chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

Comparative study of structural properties of trehalose water solutions by neutron diffraction, synchrotron radiation and simulation

Neutron diffraction measurements combined with H/D substitution have been performed on trehalose aqueous solutions as a function of temperature and concentration by using the SANDALS diffractometer at ISIS Facility (UK). The findings point out a high capability of trehalose to strongly affect the tetrahedral hydrogen bond network of water. The neutron diffraction results are also compared with simulation and experimental data obtained by synchrotron radiation on the phospholipid bilayer membranes (DPPC)/trehalose/H 2O ternary system.

Acetone hydration in supercritical water: (13)C-NMR spectroscopy and Monte Carlo simulation.

The (13)C-NMR chemical shift of acetone delta((13)C[Double Bond]O) was measured in aqueous solution at high temperatures up to 400 degrees C and water densities of 0.10-0.60 g/cm(3) for the study of hydration structure in the supercritical conditions. The average number N(HB) of hydrogen bonds (HBs) between an acetone and solvent waters and the energy change DeltaE upon the HB formation were evaluated from the delta and its temperature dependence, respectively. At 400 degrees C, N(HB) is an increasing function of the water density, the increase being slower at higher water densities. The acetone-water HB formation is exothermic in supercritical water with larger negative DeltaE at lower water densities (-3.3 kcal/mol at 0.10 g/cm(3) and -0.3 kcal/mol at 0.60 g/cm(3)), in contrast to the positive DeltaE in ambient water (+0.078 kcal/mol at 4 degrees C). The corresponding Monte Carlo simulations were performed to calculate the radial and orientational distribution functions of waters around the acetone molecule. The density dependence of N(HB) calculated at 400 degrees C is in a qualitative agreement with the experimental results. In the supercritical conditions, the HB angle in a neighboring acetone-water pair is weakly influenced by the water density, because of the absence of collective HB structure. This is in sharp contrast to the hydration structure in ambient water, where the acetone-water HB formation is orientationally disturbed by the tetrahedral HB network formation among the surrounding waters.

Aggregation of water molecules: Atmospheric implications

The equilibrium constants for water oligomers ranging from dimers to cyclic hexamers are determined using Wertheim’s theory of associating systems. In the present model for water, the pair potential has a spherical hard core, and tetrahedral hydrogen bonds which are represented by an energy parameter and an interaction volume. On the basis of the present theory, one predicts that in earth’s troposphere, water dimers and perhaps trimers may contribute to the absorption of solar radiation, but concentrations of higher oligomers are too low to influence the optical properties of the earth’s atmosphere.

Hydrogen Network Fluctuations and the Microwave Dielectric Properties of Liquid Water

A short tutorial is given on interactions of water with electromagnetic fields, particularly in the microwave frequency range. Properties of the water molecule are sketched and attributes of the percolating tetrahedral hydrogen bond network of liquid water are presented. Characteristics in the polarization noise of liquid water are discussed and are related to the dielectric spectrum of water. The principal dielectric relaxation in the microwave region is represented by a Debye-type spectrum, the parameter values of which are given as a function of temperature in tabular form. At 19°C, as an example, the complex dielectric water spectrum is shown in an extended frequency range, also covering the near millimetre and submillimetre wave region up to 2 THz. A wait-and-switch model of dielectric relaxation, as suggested by computer simulation studies, is briefly outlined, in order to illustrate the mechanisms behind the hydrogen network fluctuations.

A new analytic equation of state for liquid water

We develop a new analytical equation of state for water based on the Song, Mason, and Ihm equation of state and Poole et al.’s simple model of the free energy of strong tetrahedral hydrogen bonds. Repulsive and attractive forces are modeled using a modification of the Weeks–Chandler–Anderson decomposition of the pair potential, with closed tetrahedral hydrogen bonds contributing both internal energy and entropy to the free energy of water. Strong tetrahedral hydrogen bonds are modeled explicitly using a simplified partition function. The resulting equation of state is 20–30 times more accurate than equivalent simple cubic equations of state over a wide range of pressures (0.1→3000 bar) and temperatures (−34→1200 °C) including the supercooled region. The new equation of state predicts a second liquid–liquid critical point at pC′=0.954 kbar, ρC′=1.045 g cm−3 and TC′=228.3 K. The temperature of this second critical point is above the homogeneous freezing temperature at 1 kbar, thus this region of the phase diagram may be experimentally accessible. The phase diagram also suggests that the homogeneous nucleation temperature above 1.2 kbar may be determined by a phase transition from high-density water to low-density water.

Aggregation Behavior in the Semidilute Poly(N-vinyl-2-pyrrolidone)/Water System

Dynamic and static light scattering experiments were performed on aqueous solutions of poly(N-vinyl-2-pyrrolidone) in the dilute and semidilute regime. In the dilute regime, typical good solvent behavior is found. In the semidilute regime, we observe two relaxation times in the autocorrelation functions and intense forward scattering. The short time relaxation has a typical q2 dependence, characteristic of diffusion, and the long time relaxation an approximately q3 dependence, characteristic of intraparticle dynamics. This behavior is not consistent with predicted semidilute, good solvent system behavior but instead indicates the presence of aggregates. Using combined static and dynamic scattering, we show these aggregates to be approximately 2−3 times the size of the dilute-solution radius of gyration. We attribute this anomalous behavior to the unique, tetrahedral hydrogen bond network of water and show that denaturing the water through the addition of denaturing agents known to disrupt the water structure significantly diminishes the aggregate size. We also show through pressure denaturation that the aggregation process is reversible.

Network hydrogen bonding in two new cocrystals sustained by 731-1731-1731-1, a tetrahedral hydrogen bond donor

We report details of the synthesis and X-ray crystal structures of two new cocrystals that are sustained by the tetrahedral hydrogen bond donor [Mn(CO)3(μ3-OH)]4. [Mn(CO)3(μ3-OH)]4· 2(2,3,5,6-tetramethylpyrazine)·2H2O·2MeCN,a=21.503(3),b=12.674(1),c=17.318(2), β=102.15(2), C2/c,Dcalc=1.46 mg/m3,Z=4,4188 observed reflns,Rf=0.047,Rw=0.040; 1.[Mn(CO)3(μ3-OH)]4·4,4′-dipyridyl·2MeCn,a=16.942(6),b=12.395(2),c=18.790(6), β=114.88(3), C 2/c,Dcalc=1.60 mg/m3,Z=4,2430 observed reflns,Rf=0.043,Rw=0.051;2. 1 crystallizes as a 2-D grid, whereas2 forms 1-D strands. The hydrogen bond patterns exhibited by1 and2 are analyzed in the context of our earlier studies involving [Mn(CO)3(μ3-OH)]4 and other relevant literature.

Model for the structure of the liquid water network

The state of a water molecule in liquid water is defined by its time-average network environment. Two states are characterized. State A is the familiar four-coordinated state of the Bernal-Fowler model with tetrahedral hydrogen bonds. State B is five-coordinated. Reexamination of the static dielectric constant by the method of Oster and Kirkwood confirms the marked polar character of the four-coordinated state but shows that the five-coordinated state is only about half as polar. Explicit five-coordinated models are proposed which are consistent with polarity and satisfy constraints of symmetry and hydrogen-bond stoichiometry. The potential energy due to the dipole-dipole interaction of the central water molecule with its time-average solvent network is derived without additional parameters. This permits prediction of barriers to rotation, frequencies for hindered rotation and liberation in the network, and ..delta..H/sub A,B/ and ..delta..S/sub A,B/. The results are in substantial agreement with relevant experiments. In particular, the barriers to rotation permit a consistent interpretation of the dielectric relaxation spectrum. The relative importance of the two states varies predictably with the property being examined, and this can account for some of the schizophrenia of aqueous properties. Since the two-state model is based on time-average network configurations, it does not applymore » when the time scale of observation is short compared to network frequencies, i.e., at infrared frequencies where continuum models may be successful.« less