单笼形水分子簇中心水分子对类型关系

随机产生单笼形水分子簇(H2O)n(n=8~36),经分类统计后发现,在笼形水分子簇中,其1221,1212,2121和2112四类氢键的个数与水分子和氢键总数之间有定量关系,且1212类氢键的个数与2121类的氢键始终相等.如果笼形水分子簇中某一类氢键数已知,则它的其余三类氢键的个数也随即确定.     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

Thermodynamic functions of liquid water calculated from the temperature evolution of the vibration spectrum contour

Configurational contributions of hydrogen bonds to thermodynamic properties of water (internal energy, entropy, and heat capacity) are calculated on the basis of statistical distributions of frequencies of the OH vibrations of liquid water, calculated earlier from the experimental Raman spectra in frameworks of the fluctuation theory of hydrogen bonding. Distributions of the energy of hydrogen bonds are determined. It is shown by comparison with computer experiments that previously established dependence of energy on frequency, E(nu), must be considered in this formalism as the effective energy of hydrogen bonding averaged over those configurations of hydrogen bridge O-H...O which lead to the given frequency nu in the vibrational spectrum. Contribution of van der Waals interactions not affecting the frequency shift to heat capacity is evaluated.     

Spectroscopic characterization of microscopic hydrogen-bonding disparities in supercritical water

The local hydrogen-bonding environment in supercritical water (380 degrees C, 300 bars, density 0.54 gcm3) was studied by x-ray Raman scattering at the oxygen K edge. The spectra are compared to those of the gas phase, liquid surface, bulk liquid, and bulk ice, as well as to calculated spectra. The experimental model systems are used to assign spectral features and to quantify specific local hydrogen-bonding situations in supercritical water. The first coordination shell of the molecules is characterized in more detail with the aid of the calculations. Our analysis suggests that approximately 65% of the molecules in supercritical water are hydrogen bonded in configurations that are distinctly different from those in liquid water and ice. In contrast to liquid water the bonded molecules in supercritical water have four intact hydrogen bonds and in contrast to ice large variations of bond angles and distances are observed. The remaining approximately 35% of the molecules exhibit two free O-H bonds and are thus either not involved in hydrogen bonding at all or have one or two hydrogen bonds on the oxygen side. We determine an average O-O distance of 3.1+/-0.1 A in supercritical water for the H bonded molecules at the conditions studied here. This and the corresponding hydrogen bond lengths are shown to agree with neutron- and x-ray-diffraction data at similar conditions. Our results on the local hydrogen-bonding environment with mainly two disparate hydrogen-bonding configurations are consistent with an extended structural model of supercritical water as a heterogeneous system with small patches of bonded molecules in various tetrahedral configurations and surrounding nonbonded gas-phase-like molecules.     

Molecular dynamic simulation of sub- and supercritical water with new interaction potential

Molecular dynamic simulation of water under sub- and supercritical conditions was performed with a new form of O···H pairwise potential with an additional non-electrostatic term corresponding hydrogen bond formation. Some structural properties of water and hydrogen bonds characteristics were calculated in a wide temperature range and pressure 50 MPa. Dependences of these values on temperature were analyzed.     

Proper and improper hydrogen bonds in liquid water

The total lifetime distributions for hydrogen bonds in snapshots of molecular dynamics simulations of water serve as a basis to identify a class of proper hydrogen bonds. Proper bonds emerge and break up when restructuring the surrounding area of the hydrogen bond networkwhich weakly depend on the properties of this individual bond, i.e., almost randomly. Therefore, the distribution of the bond lifetimes is described by an exponential function similar to the distribution of the mean free path time in gas. It is shown that proper hydrogen bonds are strong, long-lived, and tetrahedrally oriented bonds. They account for about 80% of the bonds in each snapshot. Thus, these bonds form the basis or framework of the hydrogen bond network of water. The other, improper bonds have a substantially shorter lifetime; these are weak, bifurcated, and quickly switching bonds.     

Thermodynamics of water sorption in acrylic homonetworks and IPNs

The equilibrium thermodynamic properties of poly(hydroxyethyl acrylate) and poly(ethyl acrylate)-i-poly(hydroxyethyl acrylate) hydrogels are investigated starting from the water sorption isotherms of the systems. Partial enthalpy and entropy of the sorbed water in the gel differ markedly from the values of pure water at the lowest water contents, and tend to those of liquid water as saturation is approached. The residual mixing free energy is calculated, as a means of assessing the intensity of the water-polymer interaction. Its small positive magnitude shows that water-polymer hydrogen bonds are labile compared to water-water and polymer-polymer hydrogen bonds, and thus the stability of the gel state is still mainly due to the combinatorial entropic contribution to the mixing free energy. An equation correctly describing the sorption isotherms, when combined with the thermodynamic equations, can deliver the true water-polymer interaction parameter and its dependence on the polymer volume fraction in the gel.     

Computer simulation of the hydrogen bond lifetime and the mechanism of the structural rearrangement of water

The concept of a hydrogen bond lifetime is analyzed in a computer experiment. It is shown that different definitions of the lifetime of a hydrogen bond characterize definite stages in the microdynamics of a liquid. The lifetimes of hydrogen bonds are calculated for water using the TIP4P and TIP4B-HB model potentials. A number of features in the mechanism of the structural rearrangement of the nearest surrounding is determined by comparing them.     

The contribution of hydrogen bonds to the surface tension of water

The surface energy, the surface free energy and the surface entropy of liquid water are calculated from the decrease in the number of hydrogen bonds in the surface layer, estimated on the bash of a simplified aater structure scheme. In the calculations of the free energy density function only the hydrogen-bond interactions between molecules are taken into consideration. The resulting surface free energy of water is ≈43 mN/m at 25°C. The calculated temperature dependence is consistent with that observed.     

Hydration free energies and entropies for water in protein interiors

Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Two different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI) and in the I76A mutant of barnase, represent very different environments for the water molecule: one which is polar, forming four water-protein hydrogen bonds, and one which is more hydrophobic, forming only one water-protein hydrogen bond. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the nonpolar cavity is entropically favorable. For both proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increased length and weakened strength of protein-protein hydrogen bonds near the cavity.     

Structure and dynamics of water in mixed solutions including laponite and PEO

To investigate the structure and dynamics of water in mixed solutions including laponite clay particles and poly(ethylene oxide) (PEO), we measured the Raman spectra of the mixed solutions in the temperature range 283-313 K. The results show that the vibrational energies of the O-H stretching modes in the mixed solutions depend on the water content and temperature. The energy shifts of the O-H stretching modes are attributed to changes in the water structure. By applying a structural model of bulk water to the spectra in the O-H stretching region, the local structures of water in the solutions were analyzed. The result shows that the formation probability of hydrogen bonds in the solutions decreases as the water content decreases. Laponite and PEO have effects to disrupt the network structure of hydrogen bonds between water molecules. Further, it was found that laponite and PEO cause increase in the strength of hydrogen bonds of surrounding water,although the strength of the hydrogen bonds increases with the order water-laponite < water-water < water-PEO. It is concluded that water in laponite-PEO mixed solutions has a less-networked structure with strong hydrogen bonds compared with bulk water.     

Hydrogen bond lifetime in supercritical water

Molecular dynamics simulations of water were performed in a wide range of supercritical temperatures and pressures with using TIP4P-HB model potential. The effect of state parameters on microdynamics of hydrogen bonds was studied. Isobaric (P = 30, 50, 80, 100 MPa) and isothermal (T = 673 K) dependencies of average hydrogen bond lifetime were calculated.     

Multi-centred hydrogen bonds between water and perchlorate anion

Results of classical molecular dynamics simulations are presented for the re-orientational dynamics of water hydrogen bonded to perchlorate anion. Different mechanisms of bond formation are presented. Due to its regular tetrahedron geometry the perchlorate anion can make classical as well as bifurcated and trifurcated hydrogen bonds. The angular variation of water in the first solvation shell of perchlorate suggests the transitional character of multi-centred hydrogen bonds. As a result water molecules can slide around the anion.     

Antisymmetry and stability of water systems. I. Planar cyclic clusters

All topologically distinct configurations of planar cyclic water clusters consisting of three to six molecules are calculated. The symmetry of configurations is analyzed using an additional operation of antisymmetry that changes the directions of all hydrogen bonds. It is concluded that the concept of antisymmetry and the presence of similar in properties but inequivalent “configurations-antipodes” reflects a new fundamental feature of water systems, namely, the internal molecular asymmetry.     

甘油水溶液氢键特性的分子动力学模拟

为了研究低温保护剂溶液的结构和物理化学特性, 以甘油为保护剂, 采用分子动力学方法, 对不同浓度的甘油和水的二元体系进行了模拟. 得到了不同浓度的甘油水溶液在2 ns内的分子动力学运动轨迹, 通过对后1 ns内运动轨迹的分析, 得到了各个原子对的径向分布函数和甘油分子的构型分布. 根据氢键的图形定义, 分析了氢键的结构和动力学特性. 计算了不同浓度下体系中平均每个原子(O和H)和分子(甘油和水)参与氢键个数的百分比分布及其平均值. 同时还计算了所有氢键、水分子之间的氢键以及甘油与水分子之间的氢键的生存周期.     

Properties of the network of the hydrogen bonds of water

Networks of the hydrogen bonds and those consisting of lines connecting nearby molecules were constructed using configurations of water molecules obtained by the Monte-Carlo method. The concentrations of closed cycles of hydrogen bonds were established to be determined only by the probability of hydrogen bond formation. Characteristics of a model ideal water network were determined. Topological properties of the Polk model and those of the network of nearest neighbors substantially differ from the properties of the ideal network. The totality of the hydrogen bonds in pure water was proposed to be considered as a hierarchical system. Three topologically different structures of water associates were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 928–931, May, 1997.     

A DFT-based study of the hydrogen-bonding interactions between epicatechin and methanol/water

Tea polyphenols are essential components that give tea its medicinal properties. Methanol and water are frequently used as solvents in the extraction of polyphenols. Hydrogen-bonding interactions are significant in the extraction reaction. Density functional theory (DFT) techniques were used to conduct a theoretical investigation on the hydrogen-bonding interactions between methanol or water and epicatechin, an abundant polyphenol found in tea. After first analyzing the epicatechin monomer's molecular geometry and charge characteristics, nine stable epicatechin (EC) H₂O/CH₂OH complex geometries were discovered. The presence of hydrogen bonding in these improved structures has been proven. The calculated hydrogen bond structures are very stable, among which the hydrogen bond bonded with a hydroxyl group has higher stability. The nine complex structures’ hydrogen bonds were thought to represent closed-shell-type interactions. The interaction energy with 30O-31H on the epicatechin benzene ring is the strongest in the hydrogen bond structure. While the other hydrogen bonds were weak in strength and mostly had an electrostatic nature, the hydrogen bonds between the oxygen atoms in H₂O or CH₂OH and the hydrogen atoms of the hydroxyl groups in epicatechin were of moderate strength and had a covalent character. Comparing the changes in the hydrogen bond structure vibration peak, the main change in concentration peak is the hydrogen bond vibration peak in the complex. Improved the study on the hydrogen bond properties of CH₂OH and H₂O of EC.     

Weakly and strongly associated nonfreezable water bound in bones

Water bound in bone of rat tail vertebrae was investigated by ¹H NMR spectroscopy at 210–300 K and by the thermally stimulated depolarization current (TSDC) method at 190–265 K. The ¹H NMR spectra of water clusters were calculated by the GIAO method with the B3LYP/6-31G(d,p) basis set, and the solvent effects were analyzed by the HF/SM5.45/6-31G(d) method. The ¹H NMR spectra of water in bone tissue include two signals that can be assigned to typical water (chemical shift of proton resonance δ_H = 4–5 ppm) and unusual water (δ_H = 1.2–1.7 ppm). According to the quantum chemical calculations, the latter can be attributed to water molecules without the hydrogen bonds through the hydrogen atoms, e.g., interacting with hydrophobic environment. An increase in the amount of water in bone leads to an increase in the amount of typical water, which is characterized by higher associativity (i.e., a larger average number of hydrogen bonds per molecule) and fills larger pores, cavities and pockets in bone tissue.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.