Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds

The Monte Carlo method is used to calculate spatial distribution functions of oxygen and hydrogen atoms within a large-size water model (33666 SPC/E water molecules) under atmospheric pressure at room temperature. The work focuses on structural interpretation of local densities of water at the distances of about 3–5 Å from its molecules. The distribution of the distances between water molecules connected by chains of two or more hydrogen bonds indicates that the molecules between the first and second peaks of the radial distribution function (RDF) are mainly second and, to a lesser extent, third neighbors along the chain of bonds.     

特殊缔合体系TFE水溶液分子动力学模拟

三氟乙醇(TFE)水溶液是一类特殊的缔合体系. 采用分子动力学模拟方法结合核磁共振化学位移研究了TFE水溶液体系全浓度范围的氢键网络, 并对动力学模拟结果和核磁共振化学位移进行了比较. 从径向分布函数(RDF)发现, TFE水溶液中存在着强氢键, 而体系中的C—H…O弱相互作用较为明显, 也不能忽略. 氢键网络分析发现TFE 水溶液体系的氢键大致分为以下三个区域: 在水富集区域, 水分子倾向于自身缔合形成稳定的簇结构, 随着TFE 浓度的增加, 水的有序结构受到破坏, 水分子和TFE分子发生交叉缔合作用形成氢键; 在TFE富集区域, 水分子较少, TFE分子自身通过氢键形成多缔体结构. 此外, 分子动力学统计的平均氢键数的变化和文献报导的核磁共振化学位移变化趋势相同, 实验和理论的结果吻合较好.     

水、甲醇和乙醇液体微结构性质的Car-Parrinello 分子动力学模拟

采用Car-Parrinello 分子动力学(CPMD)方法分别研究了水、甲醇和乙醇的液体微结构性质.研究结果显示:在水、甲醇和乙醇三个体系中O…O径向分布函数曲线的第一个峰位置分别为0.278、0.276 和0.275nm; O…H径向分布函数曲线的第一个峰位置分别为0.178、0.176和0.177 nm.表明基团(氢原子、甲基、乙基)的差异对O…O第一个峰的位置影响很小.但基团的差异对径向分布函数峰高的影响却很显著,由水到乙醇第一个峰的高度逐渐变高.空间分布函数表明氧原子和氢原子在溶剂分子周围有取向地分布,这与径向分布函数所表现出尖锐的第一个峰相一致.氢键分布分析显示,水、甲醇和乙醇的平均氢键数分别为3.62、1.99 和1.87,表明水形成了网状氢键结构,而甲醇、乙醇形成链状氢键结构.     

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.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

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.     

The effects of electronic polarization on water adsorption in metal-organic frameworks: H(2)O in MIL-53(Cr)

The effects of electronic polarization on the adsorption of water in the MIL-53(Cr) metal-organic framework are investigated using molecular dynamics simulations. For this purpose a fully polarizable force field for MIL-53(Cr) was developed which is compatible with the ab initio-based TTM3-F water model. The analysis of the spatial distributions of the water molecules within the MIL-53(Cr) nanopores calculated as a function of loading indicates that polarization effects play an important role in the formation of hydrogen bonds between the water molecules and the hydroxyl groups of the framework. As a result, large qualitative differences are found between the radial distribution functions calculated with non-polarizable and polarizable force fields. The present analysis suggests that polarization effects can significantly impact molecular adsorption in metal-organic frameworks under hydrated conditions.     

Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and 'free' water molecules emerge at the concentration of around 54%.     

Computer simulation of cellulose solvation in polar solvents

The solvation of cellulose molecules in water and N-methylmorpholine N-oxide has been investigated by the molecular-dynamics method. An analysis of simulation results yields the conformational characteristics of cellulose molecules in these solvents: the mean-square distance between polymer chain ends and the radial distribution function of monomer units. The radial distribution functions of oxygen atoms of solvents relative to protons of carbohydrate molecules are estimated. This step makes it possible to draw conclusions about the number and character of hydrogen bonds and the local structure of solvate shells.     

Structure and hydration of L-proline in aqueous solutions

The structure and hydration of L-proline in aqueous solution have been investigated using a combination of neutron diffraction with isotopic substitution, empirical potential structure refinement modeling, and small-angle neutron scattering at three concentrations, 1:10, 1:15, and 1:20 proline/water mole ratios. In each solution the carboxylate oxygen atoms from proline accept less than two hydrogen bonds from the surrounding water solvent and the amine hydrogen atoms donate less than one hydrogen bond to the surrounding water molecules. The solute-solute radial distribution functions indicate relatively weak interactions between proline molecules, and significant clustering or aggregation of proline is absent at all these concentrations. The spatial density distributions for the hydration of the COO- group in proline show a similar shape to that found previously in L-glutamic acid in aqueous solution but with a reduced coordination number.     

Solvation Properties of Aliphatic Alcohol–Water and Fluorinated Alcohol–Water Solutions for Amide Molecules Studied by IR and NMR Techniques

Solvation properties of aliphatic alcohol–water and fluorinated alcohol–water solutions were probed by amide molecules as solutes using infrared (IR) and ¹H and ¹³C NMR techniques. These include four alcohols: ethanol (EtOH), 2-propanol (2-PrOH), 2,2,2-trifluoroethanol (TFE), and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and three amides: N-methylformamide (NMF), N-methylacetamide (NMA) and N-methylpropionamide (NMP). The hydrogen bonds of the amide carbonyl oxygen with water are gradually weakened as the alcohol content increases. This decreases in the order of HFIP > TFE ≈ 2-PrOH > EtOH. In TFE– and HFIP–water solutions, the hydrogen bond between the amide amino hydrogen and water is also gradually broken with increasing x _A. This trend is more notable in the order of NMP > NMA > NMF. The hydrophobic moieties of the amide methyl and ethyl groups are solvated by the fluoroalkyl groups of fluorinated alcohols due to the hydrophobic interaction among them. Thus, the steric hindrance generated by the solvated alkyl group of amides promotes the breaking of the hydrogen bonds between amide and water.     

Monte Carlo simulation of liquid hydroxylamine using ab initio intermolecular potential functions

A potential model for intermolecular interactions between hydroxylamine (NH₂OH) molecules based on ab initio quantum mechanical calculations is reviewed and critically assessed by analyzing results from a Monte Carlo simulation of liquid hydroxylamine. The liquid structure is studied in detail using radial, energy, and angular distribution functions, coordination numbers, and their distribution. Results indicate a large first solvation shell (5.3 Å), which contains 13 molecules, out of which only 4 are truly bonded by nonlinear, low-energy hydrogen bonds. These are of either the OH…O or the OH…N type, as NH…O and NH…N linear bonds are considerably suppressed, and no cyclic dimers are found. The dependence of the structural and physical properties on the simulation characteristics has also been investigated.     

Molecular dynamics simulations of atomistic hydration structures of poly(vinyl methyl ether)

Molecular dynamics simulations have been performed on the aqueous solutions of poly(vinyl methyl ether) (PVME) at various concentrations. Both radial and spatial distribution functions are used to investigate the detailed hydration structures. The structures of water are found to get increasingly concentrated when polymers are introduced and the water motions are severely hindered by the polymer matrix. At low concentrations, larger populations of tt conformers in meso dyads than those at higher concentrationsare found and this phenomenon is believed to be due to the increasing in bonding of water molecule to two ether oxygens in meso dyad. At higher concentrations, the size and conformations of polymers are quite similar to those in bulk. A transition of hydrogen bond fractions between PVME and water at around the concentration of 0.3 is observed and this value is perfectly in agreement with the results of conformational analysis and Raman spectra. Second neighbor hydrogen bond statistics revealed the domination of complicated hydrogen bond networks at low concentrations, but single hydrogen bonds as well as isolated clusters composed of 2-4 water molecules are usual around each polymer repeat unit.     

Solvation free energies and hydration structure of N-methyl-p-nitroaniline

Solvation Gibbs energies of N-methyl-p-nitroaniline (MNA) in water and 1-octanol are calculated using the expanded ensemble molecular dynamics method with a force field taken from the literature. The accuracy of the free energy calculations is verified with the experimental Gibbs free energy data and found to reproduce the experimental 1-octanol∕water partition coefficient to within ±0.1 in log unit. To investigate the hydration structure around N-methyl-p-nitroaniline, an independent NVT molecular dynamics simulation was performed at ambient conditions. The local organization of water molecules around the solute MNA molecule was investigated using the radial distribution function (RDF), the coordination number, and the extent of hydrogen bonding. The spatial distribution functions (SDFs) show that the water molecules are distributed above and below the nitrogen atoms parallel to the plane of aromatic ring for both the methylamino and nitro functional groups. It is found that these groups have a significant effect on the hydration of MNA with water molecules forming two weak hydrogen bonds with both the methylamino and nitro groups. The hydration structures around the functional groups in MNA in water are different from those that have been found for methylamine, nitrobenzene, and benzene in aqueous solutions, and these differences together with weak hydrogen bonds explain the lower solubility of MNA in water. The RDFs together with SDFs provide a tool for the understanding the hydration of MNA (and other molecules) and therefore their solubility.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: structural, electronic, and dynamical properties

The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.     

Computational study of structural and dynamical properties of formamide-water mixtures

A molecular dynamics simulation study of structural and dynamical properties in liquid mixtures of formamide and water is presented. Site-site radial pair distribution functions, local mole fractions, pair energy distributions, and tetrahedral orientational order are the quantities analyzed to investigate the local structure in the simulated mixtures, along with a review of the intermolecular structure in terms of the distribution of hydrogen bonds. Our results indicate that there is a substitution of formamide molecules by water in the hydrogen bonds and a formation of a common hydrogen bond network. By analyzing the extent of tetrahedral order in the liquid as a function of composition, it is observed that whereas the tetrahedral network of liquid water is progressively lost by increasing the formamide concentration, the water structure within the first coordination shell is preserved and somewhat enhanced. The hydrogen-bond mean lifetimes were estimated by performing a time integration of the autocorrelation functions of bond occupation numbers. The lifetimes associated with hydrogen bonds between water, formamide, and interspecies pairs are found to increase with increasing formamide concentration. The lifetimes of the water hydrogen bonds show the largest variations, supporting the picture of an enhancement of the water structure among the nearest neighbors within the first coordination shell. We have used two different force field models for water, SPC/E [J. C. Berendsen et al., J. Phys. Chem. 91, 6269 (1987)] and TIP4P/2005 [J. L. F. Abascal and C. Vega, J. Chem. Phys. 123, 234505 (2005)]. Our results for structural and dynamical properties yield very small differences between those models, the TIP4P/2005 predicting a slightly more structured liquid and, consequently, exhibiting a slightly slower translational and librational dynamics.     

Nonideality in diffusion of ionic and hydrophobic solutes and pair dynamics in water-acetone mixtures of varying composition

We have performed a series of molecular dynamics simulations of water-acetone mixtures containing either an ionic solute or a neutral hydrophobic solute to study the extent of nonideality in the dynamics of these solutes with variation of composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to change nonmonotonically with the composition of the mixtures showing strong nonideality of their dynamics. Also, the extent of nonideality in the diffusion of these charged solutes is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and acetone molecules in these mixtures which show a somewhat similar changes in the solvation characteristics of charged and dipolar solutes with changes of composition of water-acetone mixtures. The diffusion of the hydrophobic solute, however, shows a monotonic increase with increase of acetone concentration showing its different solvation characteristics as compared to the charged and dipolar solutes. The links between the nonideality in diffusion and solvation structures are further confirmed through calculations of the relevant solute-solvent and solvent-solvent radial distribution functions for both ionic and hydrophobic solutes. We have also calculated various pair dynamical properties such as the relaxation of water-water and acetone-water hydrogen bonds and residence dynamics of water molecules in water and acetone hydration shells. The lifetimes of both water-water and acetone-water hydrogen bonds and also the residence times of water molecules are found to increase steadily with increase in acetone concentration. No maximum or minimum was found in the composition dependence of these pair dynamical quantities. The lifetimes of water-water hydrogen bonds are always found to be longer than that of acetone-water hydrogen bonds in these mixtures. The residence times of water molecules are also found to follow a similar trend.     

Structure and dynamics of water surrounding the poly(methacrylic acid): a molecular dynamics study

All-atom molecular dynamics simulations are used to study a single chain of poly(methacrylic acid) in aqueous solutions at various degrees of charge density. Through a combination of analysis on the radial distribution functions of water and snapshots of the equilibrated structure, we observe that local arrangements of water molecules, surrounding the functional groups of COO- and COOH in the chain, behave differently and correlated well to the resulting chain conformation behavior. In general, due to strong attractive interactions between water and charged COO- via the formation of hydrogen bonds, water molecules tend to form shell-like layers around the COO- groups. Furthermore, water molecules often act as a bridging agent between two neighboring COO- groups. These bridged water molecules are observed to stabilize the rodlike chain conformation that the highly charged chain reveals, as they significantly limit torsional and bending degrees of the backbone monomers. In addition, they display different dynamic properties from the bulk water. Both the resulting oxygen and hydrogen spectra are greatly shifted due to the presence of strong H-bonded interactions.     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.