Effects of ion atmosphere on hydrogen-bond dynamics in aqueous electrolyte solutions

We have performed a series of molecular dynamics simulations of aqueous NaCl and KCl solutions at different concentrations to investigate the effects of ion atmosphere on the dynamics of water-water hydrogen bonds at room temperature. The average number of hydrogen bonds per water molecule decreases with increase of ion concentration. The dynamics of hydrogen-bond breaking is found to accelerate somewhat and that of hydrogen-bond structural relaxation, which occurs at a longer time scale, is found to slow down with increasing ion concentration for both NaCl and KCl solutions.     

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TMU. The lifetime and structural relaxation time of water–water and NMA–water hydrogen bonds show a strong increase with the addition of TMAO and TMU in the solution, whereas the change is nominal in case of urea solution. It is also found that the translational and rotational dynamics of water and NMA slowdown with increasing the concentration of these osmolytes. The slower dynamics of water and NMA is more pronounced in case of TMAO and TMU solution, as these co-solutes strengthen the average hydrogen bond energies between water–water and NMA–water, whereas urea has a little effect on the hydrogen bonding structure and dynamics of aqueous NMA solution. The calculated self-diffusion coefficient values for water and these co-solutes are in similar pattern with experimental observations.     

Dipolar response and hydrogen-bond kinetics in liquid water in square-wave time-varying electric fields

Non-equilibrium molecular dynamics simulations of liquid water have been performed at 298 K in the presence of external time-varying electric fields, approximating a square wave, of varying peak intensity (0.005–0.1 V/Å) in the microwave to far-infrared frequency range (20–500 GHz). Significant non-thermal field effects were noted in terms of dipolar response and acceleration of hydrogen-bond kinetics. The coupling between the total dipole moment and the external field has been investigated and autocorrelation functions (ACFs) of both the total dipole moment and the average of the individual molecular dipole moment along the laboratory axis of the applied fields exhibited coupling, with the former showing a stronger coupling and the latter showing coupling to lower magnitude fields. The maximum alignment achieved has been computed as a function of field intensities and frequencies: the lower frequencies show a greater maximum alignment as the system had more time within each field cycle to respond. The normalised probability distribution and the hydrogen-bond ACFs have been computed: the ACF showed a clear effect over shortening the hydrogen-bond relaxation time. The field effects over the molecules’ transitions from four to five hydrogen bonds have been computed. There was an enhancement of fewer molecules undergoing transitions and a dampening for a larger proportion of molecules, depending on the external fields’ periods.     

Enhancement of water self-diffusion at super-hydrophilic surface with ordered water

It has been well acknowledged that molecular water structures at the interface play an important role in the surface properties, such as wetting behavior or surface frictions. Using molecular dynamics simulation, we show that the water self-diffusion on the top of the first ordered water layer can be enhanced near a super-hydrophilic solid surface. This is attributed to the fewer number of hydrogen bonds between the first ordered water layer and water molecules above this layer, where the ordered water structures induce much slower relaxation behavior of water dipole and longer lifetime of hydrogen bonds formed within the first layer.     

Hydrogen-bond dynamics near a micellar surface: origin of the universal slow relaxation at complex aqueous interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.     

Structure and dynamics of water: from ambient to supercritical

Our recent works on supercritical water are reviewed. In order to elucidate the hydrogen bonding state of supercritical water, the proton chemical shift of the water proton is measured at temperatures up to 400 °C and densities of 0.19, 0.29, 0.41, 0.49, and 0.60 g/cm³. The magnetic susceptibility correction is made in order to express the chemical shift relative to an isolated water molecule in dilute gas. The chemical shift is then related to the average number of hydrogen bonds in which a water molecule is involved. It is found that the hydrogen bonding persists at supercritical temperatures and that the average number of hydrogen bonds is at least one for a water molecule at the densities larger than the critical. The density dependence of the chemical shift at supercritical temperatures is analyzed on the basis of statistical thermodynamics. It is shown that the hydrogen bonding is spatially more inhomogeneous at lower densities. The dipole moment of water at supercritical states is also estimated from the number of hydrogen bonds. The dynamical counterpart of our structural study of supercritical water has been performed by NMR relaxation measurements. Using D₂O, we measured the spin-lattice relaxation time and determined the reorientational relaxation time as a function of the water density and temperature. It is then found that while the reorientational relaxation time decreases rapidly with the temperature in the subcritical condition, it is a weak function of the density in the supercritical conditions.     

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

The effects of salt concentrations on the structure, dynamics and hydrogen bond structural relaxation properties of ～1.10 M aqueous N-methylacetamide (NMA) solution at 308 K are studied by classical molecular dynamics simulations. We have considered the concentration range of salts solution from 0.222 to 3.756 M to investigate the behaviour of aqueous environment of peptide bonds in the presence of concentrated NaCl and KCl solution. It is found that the addition of salt solution facilitates the structural breaking of aqueous NMA hydrogen bonds, as a result the number of hydrogen bonds per NMA molecule and their stability decreases. The water and NMA molecule shows slower translational and rotational dynamics with increasing salt concentrations due to additional ion atmospheric friction. Our result shows that the cation–O_NMA radial distribution function decreases whereas the Cl^?─H_NMA radial distribution function increases with ion concentration. On the other hand, the cation–O_water and Cl^?─H_water radial distribution function shows very negligible change with respect to ion concentration. We have also calculated NMA–water and water–water hydrogen bond structural relaxation times. It is observed that the hydrogen bond structural relaxation of O_NMA─H_water is comparatively slower than the H_NMA─O_water hydrogen bond, which can be attributed to higher number and greater stability of the former hydrogen bond than the latter. The change of the dynamical quantities observed here is more prominent in addition of NaCl rather than the KCl solution.     

界面氢键对受限水结构和动态特性的影响

应用反应力场分子动力学方法, 模拟了水限制在全羟基化二氧化硅晶体表面间的弛豫过程, 研究了基底表面与水形成的界面氢键, 及其对受限水结构和动态特性行为的影响. 当基底表面硅醇固定时, 靠近基底表面水分子中的氧原子与基底表面的氢原子形成强氢键, 这使得靠近表面水分子中的氧原子比对应的氢原子更靠近基底表面, 从而水分子的偶极矩远离表面. 当基底表面硅醇可动时, 靠近基底表面水分子与基底表面原子形成两种强氢键, 一种是水分子中的氧原子与表面的氢原子形成的强氢键, 数量较少, 另一种是水分子中的氢原子与表面的氧原子形成的强氢键, 数量较多, 这使得靠近表面水分子中的氢原子比对应的氧原子更靠近表面, 从而水分子的偶极矩指向表面. 在相同几何间距下, 当基底表面硅醇可动时, 表面的活动性使得几何限制作用减弱, 导致了受限水分层现象没有固定表面限制下的明显. 此外, 固定表面比可动表面与水形成的界面氢键作用较强, 数量较多, 导致了可动表面限制下水的运动更为剧烈.     

Water in porous glasses. A computer simulation study

We report molecular dynamics simulations of water confined in a cylindrical silica pore. The pore geometry and size is similar to that of typical pores in porous Vycor glass. In the present study we focus on the dependence of microscopical structural and dynamical properties on the degree of hydration of the pore. We have performed five simulations of systems between 19 and 96 % hydration. In all cases, water adsorbs strongly on the pore surface, clearly demonstrating the hydrophilic nature of the Vycor surface. Two layers of water molecules are affected strongly by the interactions with the glass surface. With decreasing degree of hydration an increasing volume in the center of the pore is devoid of water molecules. At 96 % hydration the center is a continuous and homogeneous region that has, however, a lower density than bulk water at ambient conditions. A well-pronounced mobility profile exists, where molecules in the center of the pores have substantially higher self diffusion coefficients than molecules on the pore surface. The spectral densities of center of mass and hydrogen atom motion show the signature of confinement for the molecules close to the pore surface, while the spectral densities in the center of the pore are similar to those in bulk water. The molecular dynamics results are in good agreement with recent experiments. Our data indicate that the dependence of experimental data on the level of hydration of the Vycor sample is due to the different relative contribution of molecules adsorbed on the pore surface and bulk-like molecules in the interior of the pore to the experimental averages.     

Dynamics and hydrogen bonding in liquid ethanol

Molecular dynamics simulations of liquid ethanol at three temperatures have been carried out. The hydrogen bonding states of ethanol molecules have been characterized by the number of hydrogen bonds in which the molecules participate. It is observed that the mean lifetimes of molecules in each hydrogen bonding state are markedly dependent on the temperature. Moreover, molecules with one hydrogen bond are more stable when they are donors than when they are acceptors. The dependence of the reorientational correlation functions on the hydrogen bonding state of molecules has been studied carefully. The decay of these functions is slower for molecules with higher numbers of hydrogen bonds and also becomes slower as temperature decreases. The relaxation for molecules with only one hydrogen bond is faster for those acting as proton donors than for those acting as proton acceptors. Finally, the results obtained by computer simulation are compared with those from recent measurements of the frequency-dependent dielectric permittivity of liquid ethanol.     

Anomalously soft dynamics of water in a nanotube: a revelation of nanoscale confinement

Quasi-one-dimensional water encapsulated inside single-walled carbon nanotubes, here referred to as nanotube water, was studied by neutron scattering. The results reveal an anomalously soft dynamics characterized by pliable hydrogen bonds, anharmonic intermolecular potentials, and large-amplitude motions in nanotube water. Molecular dynamics simulations consistently describe the observed phenomena and propose the structure of nanotube water, which comprises a square-ice sheet wrapped into a cylinder inside the carbon nanotube and interior molecules in a chainlike configuration.     

Investigation of the adsorption mechanism of water nanocluster on the substrate: The size and interaction strength effect

Molecular dynamics simulation is utilized to investigate the effects of both the size of a water nanocluster and the interaction strength between the water nanocluster and a solid surface on the dynamic behavior of the water nanocluster when it is adsorbed on a solid surface. The simulation results demonstrate that both the size and the interaction strength influence the adsorption behavior of the water nanocluster on the substrate. When the interaction strength between water molecules and the substrate is strong, the morphology of the water nanocluster adsorbed on the substrate will tend to be flatter in shape. However, when the interaction strength is weak, the morphology of the water nanocluster is a semi-spherical shape. The size of the water nanocluster causes the water molecules in the first layer to lay flatter on the substrate at stronger interaction strengths. As the interaction strengths exceed 1.5 kcal mol⁻¹, the value of orientation factor will reverse its trend for water nanoclusters with different sizes, with the smaller water nanocluster having the smallest orientation factor.     

Correlations among hydrogen bonds in liquid water

By performing computer simulations of water with the TIP5P potential we show that structures formed by two or more hydrogen bonds affect the dynamical and static properties of water, especially in the vicinity of freezing temperature. In particular, the short time correlation between two coupled hydrogen bonds cannot be predicted assuming the statistical independence of the single hydrogen bonds. This introduces an additional relaxation time of approximately 9 ps close to the freezing point. We also find that the time persistence of structures formed by several hydrogen bonds (the first solvation shell) correlates with the local density, which is smaller around water molecules with a long-living environment.     

Hydrogen bond dynamical properties of adsorbed liquid water monolayers with various TiO2 interfaces

Equilibrium classical molecular dynamics (MD) simulations have been performed to investigate the hydrogen-bonding kinetics of water in contact with rutile-(110), rutile-(101), rutile-(100), and anatase-(101) surfaces at room temperature (300?K). It was observed that anatase-(101) exhibits the longest-lived hydrogen bonds in terms of overall persistence, followed closely by rutile-(110). The relaxation times, defined as the integral of the autocorrelation of the hydrogen bond persistence function, were also longer for these two cases, while decay of the autocorrelation function was slower. The increased number and overall persistence of hydrogen bonds in the adsorbed water monolayers at these surfaces, particularly for anatase-(101), may serve to promote possible water photolysis activity thereon.     

Role of protein-water hydrogen bond dynamics in the protein dynamical transition

The role of water in protein dynamics has been investigated using molecular dynamics simulations of crystals and a dehydrated powder. On the 100 ps time scale, the anharmonic and diffusive motions involved in the protein structural relaxation are correlated with the protein-water hydrogen bond dynamics. The complete structural relaxation of the protein requires relaxation of the hydrogen bond network via solvent translational displacement. Inhibiting the solvent translational mobility, and therefore the protein-water hydrogen bond dynamics, has an effect on the protein relaxation similar to dehydration.     

Structure and dynamics of ordered water in a thick nanofilm on ionic surfaces

The structure and dynamics of water in a thick film on an ionic surface are studied by molecular dynamic simulations. We find that there is a dense monolayer of water molecules in the vicinity of the surface. Water molecules within this layer not only show an upright hydrogen-down orientation, but also an upright hydrogen-up orientation. Thus, water molecules in this layer can form hydrogen bonds with water molecules in the next layer. Therefore, the two-dimensional hydrogen bond network of the first layer is disrupted, mainly due to the O atoms in this layer, which are affected by the next layer and are unstable. Moreover, these water molecules exhibit delayed dynamic behavior with relatively long residence time compared with those bulk-like molecules in the other layers. Our study should be helpful to further understand the influence of water film thickness on the interfacial water at the solid-liquid interface.     

Hydrogen bonds at silica–CO2 saturated water interface under geologic sequestration conditions

To investigate the effects of sequestration condition on hydrogen bonds between mineral and water, molecular dynamics simulations have been performed. The simulations were conducted at conditions related with geologic sequestration sites: pressure (3.1–32.6 MPa), temperature (318 and 383 K), salinity (0–3 M), salt (NaCl and CaCl₂) and silica surface models Q² (geminal), Q³ (isolated) and amorphous Q³. The hydrogen bonds were classified into four types: silica–silica, silica–dissolved CO₂, silica–water as donors and silica–water as acceptors. The mean numbers of hydrogen bonds for each type were analysed. The results show that: (1) silica surface silanol groups do not form H-bonds with dissolved CO₂ molecules in water (brine); (2) The mean number of hydrogen bonds between silanol groups follows the order: Q² > amorphous Q³ > Q³; (3) The mean number of hydrogen bonds between silanol and water molecules follows the order: Q³ > amorphous Q³ > Q².     

Hydrophobic hydration at the level of primitive models. II: Large solutes and water restructuring

Details of structural changes that take place in water near an apolar solute have been studied by Monte Carlo simulations for hard sphere solutes of increasing size, including the limiting case of water at a hard structureless wall. Water has been modelled by two different types of extended primitive model, the four-site EPM4 model and five-site EPM5 model. Two different patterns of the orientational ordering of the water molecules around the solute as a function of its size have been found. For the EPM5 model, the structure of water and the orientation of its molecules near an apolar solute of finite diameter do not seem to be sensitive to the size of the solute, and only become more pronounced when the solute becomes a hard wall. On the other hand, the orientation ordering of the EPM4 molecules gradually changes with increasing size of the solute, and for solutes larger than approximately five times the size of the water molecule it is opposite to that near a small solute. A novel method to evaluate the excess chemical potential of large solutes has been implemented, and some thermodynamic quantities for water (distribution of hydrogen bonds and the excess chemical potential) have been computed as a function of the distance from the solute.     

纳米团簇熔化过程的分子动力学模拟

本文采用分子动力学结合嵌入原子多体势,模拟了不同半径的Ni纳米团簇的升温熔化过程,研究团簇尺寸对熔点和表面能的影响.模拟结果表明:团簇的熔点显著低于体材料的熔点.团簇熔化的过程首先是在团簇的表面出现预熔,然后向团簇内部扩展,直到整个团簇完全熔为液态.在模拟的纳米尺度范围内,团簇的熔点与团簇尺寸基本成线性关系.团簇的表面能随着团簇尺寸的增大而减小,而且表面能均高于体材料的表面能.     

乙醇水混合物在碳纳米管中的吸附与结构性质

用分子动力学模拟研究乙醇水混合物在碳纳米管中的结构与吸附．在(6,6)到(10,10)碳纳米管内,几乎总是充满乙醇分子,很少有水分子．在更粗的碳纳米管中有一些水分子,管内的乙醇质量分数远远高于体相值．对管内外的分子进行了径向、轴向、角向的密度和取向的分布以及氢键数目的分析．管外第一溶剂化层中分子的角向密度分布指出乙醇分子的甲基和碳壁有最强的作用,被钉扎在碳纳米管的六角形中心位置．基于对这些现象微观机制的理解,推测碳纳米管在甲醇和乙醇中更倾向吸附乙醇,通过对乙醇甲醇混合物与碳纳米管的分子动力学模拟验证了这个预测．