Hydrogen-bond dynamics of interior and surface molecules in a water nanocluster: temperature and size effects

Molecular dynamics simulations are employed to investigate the effects of temperature and size on the hydrogen-bond dynamics of interior molecules and surface molecules in a water nanocluster. The flexible three-centred (F3C) water model is invoked in the simulations. To inspect the dynamics of the interior hydrogen bonds and the surface hydrogen bonds, a spherical water nanocluster is modelled and then divided into interior molecules and surface molecules according to the density profile of the water nanocluster. It is observed that at higher temperatures the average number of hydrogen bonds decreases and yields faster hydrogen-bond relaxation for both interior molecules and surface molecules of the water nanocluster. Furthermore, the surface molecules have a lower average number of hydrogen bonds than the interior molecules. The lifetime of the surface hydrogen bonds is slightly longer than that of the interior hydrogen bonds, whereas the hydrogen-bond structural relaxation time of the surface molecules is more obviously slower than that of the interior molecules. Regarding the size effect, a larger water nanocluster is seen to have a larger average number of hydrogen bonds and a longer hydrogen-bond structural relaxation time.     

基于微流控芯片的电解质溶液太赫兹吸收特性研究

由于许多生物分子的振动和转动能级均在太赫兹波段,且太赫兹波具有电子能量低（约4 meV）,不会破坏待测样品的特性,因此可以采用太赫兹光谱技术检测生物样品。然而许多生物分子在液体环境中才能保持其生物活性,需要在盐溶液中来探究酸碱环境对其的影响,以及在盐类缓冲液中研究其生物特性。但水作为极性液体对太赫兹波有强烈的吸收,因此,探究如何减少水对太赫兹吸收的方法非常必要。水对太赫兹的吸收主要因水分子间氢键造成,现阶段最常见的方法是减少水与太赫兹波的作用距离以及破坏水分子间的氢键。利用夹心式微流控芯片在太赫兹时域光谱系统下通过观察光谱强度变化来探究电解质对水分子间氢键的影响,既减少了水和太赫兹波的作用距离,又探究了电解质对水分子间氢键的作用。在微流控芯片中分别加入不同种类以及不同浓度的电解质,通过观察其在0.1～1.0 THz范围内的光谱强度变化来分析不同电解质对水分子间氢键的影响。部分电解质促进氢键的缔合,而另一部分则破坏氢键的形成,在太赫兹光谱范围内表现为光谱强度的变化。若促进氢键的缔合则对太赫兹吸收变大,光谱强度减弱;若破坏氢键的缔合则对太赫兹吸收减弱,光谱强度增加。研究结果发现：在水中加入KCl和KBr时,太赫兹光谱强度增加,表明二者对氢键有破坏作用,使得光谱强度变大;然而当加入MgCl₂和CaCl₂时,太赫兹光谱强度减弱,表明二者对氢键有缔合作用,从而使光谱强度变小。利用太赫兹技术在0.1～1.0 THz范围内研究KCl,KBr,MgCl₂和CaCl₂这四种不同浓度的电解质溶液特性,发现它们只会对光谱强度造成一定影响,不会引入新的特征吸收峰以及对待测样品造成干扰。这对于研究诸如大肠杆菌、枯草芽孢杆菌等在0.1～1.0 THz范围内有特征吸收谱的生物分子具有一定的实用价值。在溶液中加入所需的电解质并借助微流控芯片不仅可以识别待测样品、研究待测样品的光谱信息、探究其生物特性,而且为进一步推动太赫兹技术在生化方面的应用研究提供了先决条件。     

Molecular dynamics simulations of PVP kinetic inhibitor in liquid water and hydrate/liquid water systems

The possible effects of PVP (poly(N-vinylpyrrolidone)) on the properties of liquid and water in clathrate hydrate has been investigated using NVT molecular dynamics simulations. A model for a monomer of the PVP polymer is immersed in three systems, liquid water, a unit cell of a hydrate in liquid water with a hydrate former and a third system where some of the liquid water molecules of this last system are replaced by a PVP monomer. Both molecular dynamics simulation and integral equation theory predict hydrogen bonding between the double bonded oxygen in the PVP ring and hydrogens in water. For the composite system, the PVP monomer has a preference for hydrogen bonding to hydrogens from the water molecules at the surface of the hydrate lattice. The simulations indicate that the PVP monomer tends to orient perpendicular to the hydrate surface. For the model systems in this study PVP may form hydrogen bonds with liquid water through the double bonded oxygen in the ring. When a hydrate crystal is immersed in the liquid water phase this hydrogen bonding is shifted towards the hydrate due to a more favourable Coulomb interaction involving hydrogens from more than one water molecule at the hydrate surface. The PVP monomer has a preference for perpendicular orientation with respect to the hydrate surface. A scheme is suggested for the characterization of kinetic hydrate inhibitors based on molecular dynamics simulations and on three basic properties. In addition to the energy between the active groups of the inhibitor and hydrate water another point of focus is the free energy changes in the interactions between the inhibitor and water as the charges are changed from zero to the original model charges. In particular the difference between this integral for the (hydrate water)–(PVP monomer) interaction and the (liquid water)–(PVP inhibitor) interaction should reflect the driving forces in freezing the inhibitor out from the liquid water phase and onto the hydrate surface. The third property in the characterization scheme is the diffusivities of groups connecting to the hydrate crystal, relative to the diffusivities of the hydrate crystal. Results are presented from simulations where a small cavity with a methane model as a guest is immersed in liquid water with free methane molecules at a temperature of 150K. Changes in structure, diffusivities and energy indicate a tendency towards a more solid–like structurde around the cavity.     

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.     

激光诱导等离子体对水OH伸缩振动受激拉曼散射的影响

利用532 nm脉冲激光进行水的受激拉曼散射研究,通过改变激光焦点与水-空气界面的距离,获得截然不同的OH伸缩振动受激斯托克斯和反斯托克斯谱线.焦点距水-空气界面大于20 mm时,只存在±3400cm-1的斯托克斯和反斯托克斯谱线;焦点距离水-空气界面小于20 mm时,存在±3000和±3400cm-1的斯托克斯和反斯托克斯谱线;继续缩小焦点与水-空气界面的距离,3000 cm-1谱线被增强,而3400 cm-1谱线被削弱.研究结果表明,激光诱导水产生的等离子体增强了局部水分子的氢键,导致OH伸缩振动红移,同时过剩电子增强了水的OH伸缩振动受激拉曼散射.     

A molecular level study of liquid water with a flexible water model

The structural properties of water at different temperatures and pressures have been investigated by using a flexible water model and the inherent structure mechanism. The presence of 60$^\circ$ peak in the O--O--O angle distribution function and the behaviours of the hydrogen bonds in the first shell indicate that some water molecules in the second shell move toward the central molecules through the bending (not breaking) of hydrogen bonds and even become first-shell molecules of the central molecule on the basis of the O--O cutoff distance but not first-shell molecules by means of the hydrogen-bond criterion. The inherent-structure analysis of the O--O radial distribution functions at different pressures shows that the first peak is almost independent of the pressure; the position of second peak moves from 0.45 to 0.32nm as the pressure increases from $1\times 10^5$Pa to $1\times 10^9$Pa. This particularly evident pressure effect, i.e. the constant nearest-neighbours and the transformation of outer-neighbours on the basis of O--O distance, together with the results at different temperatures, gives a positive evidence for the two-state outer-neighbour mixture model: liquid water is a mixture of Ice-Ih-type-bonding and Ice-II-type bonding structures.     

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.     

纳米MgO掺杂聚乙烯微观特性的分子动力学模拟研究

电力系统高压电缆的主要绝缘材料为聚乙烯,为了提升聚乙烯的热稳定性以及减弱水分对其的渗透能力,采用纳米MgO掺杂聚乙烯,利用分子动力学模拟方法建立包含低密度聚乙烯(LDPE)、不同颗粒半径的MgO纳米团簇以及相同质量分数水分的复合模拟模型.研究结果表明,水分会降低复合体系的玻璃化温度,MgO的掺杂则会提高复合体系的玻璃化温度,减弱聚乙烯分子链的运动并减小复合体系的自由体积,使得复合体系结构更加稳定,从而增强了聚乙烯材料的热稳定性能.此外发现水分子的扩散随着温度的上升而增大,纳米MgO的添加会与水分子形成氢键抑制水分子的扩散,同时自由体积的缩减使水分子的溶解度系数与扩散系数都减小,导致水分子的渗透能力减弱,更难以渗透进聚乙烯材料破坏其结构.研究结果可为聚乙烯的水树枝生长以及老化过程的抑制提供有益的参考.     

The fluctuation hypothesis of hydrogen bonding

To describe the distortion perturbations of the water molecules in solutions the quantum-mechanical method of partial oscillators has been developed. This method allows one to separate in a simple manner two types of influences on vibrations of OH oscillators, viz. the intermolecular perturbations resulting in the different strengths of hydrogen bonds and intramolecular coupling between stretching vibrations. Here the coupling is treated quite strictly, whereas the intermolecular perturbations are introduced phenomenologically. The calculation of the distribution of distortions among molecules in liquid H₂O and D₂O induced by non-equivalency of the two hydrogen bonds of the water molecule has been made on the basis of the method developed, and the parameters of the mean statistical molecule have been found from the experimental spectrum of HOD. The depolarization ratios of vibrations in Raman spectra of the mean statistical molecules H₂O and D₂O have been computed as an illustration of the possibilities of the proposed calculation method. All the estimates show that the stretching oscillators of H₂O and D₂O molecules are significantly coupled in spite of the great distortion of the symmetry of water molecules in the liquid state.     

Molecular mechanism of gelation upon the addition of water to a solution of poly(acrylonitrile) in dimethylsulfoxide

The solidification of a solution of poly(acrylonitrile) (PAN) in dimethylsulfoxide (DMSO) upon introduction of water into the solution is studied by Raman spectroscopy. In the absence of water, DMSO molecules are found to produce dipole-dipole bonds with PAN molecules. Upon the introduction of water, DMSO molecules produce hydrogen bonds with it and bands at 1005 and 1015 cm⁻¹ appear in the Raman spectrum, which are assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. Simultaneously, water molecules produce hydrogen bonds with PAN molecules: R-C≡N...H-O-H...N≡C-R, where R is the carbon skeleton of a PAN molecule. Accordingly, a band at 2250 cm⁻¹ arises in the Raman spectrum, which is assigned to the valence vibrations of C≡N bonds producing hydrogen bonds with a water molecule. When the water content is low and the DMSO concentration is high, the length of the hydrogen bonds varies in wide limits and the band at 2250 cm⁻¹ is wide. As the water content rises, DMSO molecules come out of PAN, the variation of the hydrogen bond length in it decreases (the band at 2250 cm⁻¹ narrows), and a high-viscosity system (gel) arises that consists of PAN molecules bonded to water molecules via “equally strong” hydrogen bonds.     

The concentration effect on the ‘hydrophobic’ and ‘hydrophilic’ behaviour around DMSO in dilute aqueous DMSO solutions. A computer simulation study

We have carried out a molecular dynamics study of dimethyl sulfoxide (DMSO) in water at 298 K at two different densities by simulating two different concentrations: 0.055 and 0.19 mole fraction. We have found an enhancement in the structure of water, an effect that becomes more pronounced as the concentration of DMSO increases. At both concentrations there is a well-defined hydration structure around the oxygen atom of DMSO, which is able to establish strong hydrogen bonds with surrounding water molecules. An increase in the concentration of DMSO depletes the solution of bulk water molecules, reducing the number of hydrogen bonds that water can have in the immediate vicinity of DMSO but increasing the strength of the hydrogen bonds made between the oxygen atom of DMSO and water. There is clear evidence of ‘hydrophobic’ hydration around the methyl groups of DMSO, which is enhanced as the concentration of DMSO increases.     

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.     

分子动力学模拟方解石和白云石润湿性

利用分子动力学模拟研究油水分子在方解石和白云石表面的吸附,分析体系的平衡构型、相对浓度、径向分布函数和吸附能,研究方解石和白云石的亲水性并对比二者差异.根据油水分子吸附规律分析方解石/白云石-油水体系作用机理.研究表明：白云石-油水体系更易达到热力学稳定状态并且体系更加稳定;方解石和白云石表面均能够优先吸附水分子并在表面形成双层结构的水膜.其中,白云石表面对水分子吸附强度大于方解石;稳定吸附过程分为两步：范德华力、静电力和O（CaCO₃,CaMg（CO₃）₂）-H（H₂O）氢键共同影响下水分子向晶体表面移动并吸附形成紧密吸附层;O（H₂O）-H（H₂O）氢键作用下游离的H₂O向晶体表面靠近形成扩散层.从分子尺度解释方解石/白云石亲水特性,为碳酸盐岩储层润湿性研究奠定理论基础.     

用分子动力学模拟甲烷水合物热激法结合化学试剂法分解

用分子动力学模拟方法研究甲烷水合物的热激法，化学试剂法，以及热激法结合化学试剂法分解，系统研究温度为277K和340K时添加液态水(WTR)和30wt％乙二醇(EG)溶液对水合物分解的影响.模拟显示WTR与水合物表面水分子形成氢键，破坏水合物原有的氢键平衡，造成笼状结构坍塌，水合物分解.EG分子中的羟基与水合物表面水分子形成氢键，从而破坏原有的稳定结构，造成水合物笼状结构被破坏，达到促进水合物分解，释放甲烷气体的效果.比较温度为277K和340K时添加WTR和30wt％EG溶液对水合物分解效果得出EG(340K)> WTR(340K)>EG(277K)>WTR(277K)，热激法结合化学试剂法能更好促进水合物分解.     

Thermally Biological Effects and Its Medical Functions of the Infrared Rays Absorbed by Living Systems

thermally biological effects of infrared lights absorbed have been studied by nonlinear quantum theory and molecular biological theory on the basis of structures of cell and water molecules. There is a large number of water in the living systems, it play an important role in living activity, and has a lot of biological functions. There would be no life without water. We can confirm that the thermally biological effect is a result produced by disorder motions of bio-water-molecules according to the essence of heat, feature of molecular structure of water, theory of molecular physics, principle of resonante absorption and experimental fact that infrared light can heat liquid water. Therefore, mechanism of this effect is that the infrared light absorbed results in the quantum vibrations of water molecules with hydrogen bonds, the vibrational energy again transformes as thermal energy of disorder motions of a great number of water molecules in the living systems. The heating waters can cause a lot of biological effects and phenomena to occur in the living systems. Therefore, the infrared lights absorbed by the living systems have some medical functions.     

醇类抑制剂对甲烷水合物形成的影响

在本工作中,甲烷水合物的生长动力学是通过甲醇、乙醇、乙二醇三种不同醇类抑制剂存在下的分子动力学模拟研究的.模拟结果发现,三种醇类都可作为甲烷水合物的抑制剂,醇类分子中的亲水性羟基极大地破坏了水合物笼的结构,并且羟基可以与局部的液态水分子形成氢键,从而增加了形成水合物笼型结构的难度,导致甲烷水合物的生长速率降低.对于甲醇分子,甲醇分子的亲水性羟基与水分子形成氢键从而破坏了水分子结构,而亲油性甲基对周围的水分子具有簇效应,两者都会降低水合物生长速率;对于乙二醇和乙醇分子,它们只含有羟基,特别是乙二醇分子含有两个羟基,其对H₂O分子有很强的吸附作用,导致水合物生长速率降低.在抑制效果方面,甲醇分子最优,乙二醇稍微优于乙醇.     

Electrons and hydrogen-bond connectivity in liquid water

The network connectivity in liquid water is revised in terms of electronic signatures of hydrogen bonds (HBs) instead of geometric criteria, in view of recent x-ray absorption studies. The analysis is based on ab initio molecular-dynamics simulations at ambient conditions. Even if instantaneous threadlike structures are observed in the electronic network, they continuously reshape in oscillations reminiscent of the and modes in ice (tau approximately 170 fs). However, two water molecules initially joined by a HB remain effectively bound over many periods regardless of its electronic signature.     

Molecular dynamics and quantum chemical approaches in the study of the hydration of protonated cyclohexyldiamines

Explicit hydration of the neutral and charged cyclohexylamine and of the cyclohexyldiamine isomers in their mono- or diprotonated forms is investigated through classical molecular dynamics (MD) simulations in aqueous solutions combined with DFT calculations in amine–water complexes. The MD studies performed in the monoamines reveal that the structure of the hydration shell around the neutral amino group (NH₂) is quite distinct from that around the charged one (NH₃⁺). On average, the number of water molecules surrounding the two groups is calculated to be ～2 and 3–4, respectively. The variation of the hydration structure prompted by the groups’ proximity is discussed based on the data found for the mono- and diprotonated diamines. To have a more detailed picture of the water molecules’ arrangement around the amino groups and of the amine–water hydrogen bonds, geometry optimisations in hydrates with up to six water molecules are carried out at the B3LYP/aug-cc-pVDZ level. Complexation energies are also computed. The main findings emerging from these calculations are found to be very helpful to rationalise the mutual influence of the amino groups and therefore to better elucidate the MD findings. The complementary nature of the two research methods is emphasised as an excellent tool in order to closely examine the hydration of polyamines, as exemplified for the cyclohexyldiamines.     

Microscopic dynamics in water and ionic aqueous solutions: velocity cross-correlations

The microscopic momentum transfer between distinct particles in water and ionic aqueous solutions has been investigated by molecular dynamics simulation. The time correlation functions between the initial velocity of a central molecule and later velocities of molecules within different coordination shells were calculated for liquid water. Special attention was paid to the influence of the intermolecular hydrogen bonds on the exchange of momentum among water molecules and on the power spectra of the velocity autocorrelation functions. The velocity cross-correlations between ions in an aqueous NaCl solution also were calculated. It was observed that the difference between the results for the Na⁺ and Cl^? ions are associated mainly with the different sizes of the ions.