Hydrogen bond networks in water and methanol with varying interaction strengths

Metropolis Monte Carlo simulations of hydrogen-bonded liquids (water and methanol) were performed with the well tested effective pair potentials TIP5P and OPLS. The Coulomb contribution for the interaction potential was damped by a factor η varied from 1 to 0.49 for water and 1 to 0.15 for methanol. As a result, the networks formed by the hydrogen-bonded molecules presented interesting properties as a function of η, including small-world patterns and percolation transitions. These complex networks were analyzed by local (clustering coefficients, average degrees), semi-global (path lengths) and global (spectral densities) properties, and islands statistics. From these properties, small-world behavior was found for η in the range 0.60-0.75 for both liquids, interestingly independent of the molecular structure of the liquid. Phase transition behavior was observed for the average degrees and the clustering coefficient curves with critical values at 0.55 for water and 0.34 for methanol. Macroscopic properties such as mass density and vaporization enthalpy were also parametrically dependent on η and they presented phase transition behavior that coincides with the critical values obtained from the topological analysis. This is probably the first time that such phase transitions are observed for these quantities and shows a direct relation between macroscopic properties and topological features of hydrogen bond networks.     

Reentrant behavior of poly(N-isopropylacrylamide) brushes in water-methanol mixtures investigated with a quartz crystal microbalance

The solvent composition induced reentrant behavior of poly(N-isopropylacrylamide) (PNIPAM) chains grafted on a SiO2 surface in water-methanol mixtures was investigated using a quartz crystal microbalance with dissipation monitoring (QCM-D) at 20 degrees C. The frequency and energy dissipation responses showed that the grafted PNIPAM chains sharply collapse when the methanol content (x(m)) reaches approximately 17 mol %. In the range 17-50 mol %, the grafted chains remain in a collapsed state. Further increase of the methanol content leads to an abrupt reswelling of the collapsed chains at x(m) > approximately 50 mol %. The sharp reentrant swelling-to-collapse-to-swelling transition was attributed to the water-methanol complexation instead of the preferential adsorption effect. Our results also suggest that the water-methanol complexation is not induced by hydrophobic interaction but by hydrogen bonding.     

Water-methanol mixtures: topology of hydrogen bonded network

Molecular dynamics simulation has been performed to study the structure of water-methanol mixtures. Besides the evaluation of partial radial distribution functions describing the hydrogen-bonded structure of the mixtures with different composition, the statistical analysis of configurations was introduced resulting in a new insight in the clustering properties and topology of hydrogen-bonded network. The results have shown that mixtures of methanol and water exhibit extended structures in solution. At low methanol concentration the water molecules form a percolated network, the methanol molecules are incorporated as monomers or short chains and together form a percolated system. In methanol-rich mixtures short water chains and longer methanol chains build up the hydrogen-bonded clusters in the system. On the basis of the statistical analysis of configurations obtained from molecular dynamics simulation it has been found that more methanol molecules are connected to non-cyclic entities, while more water molecules form rings that might have been predicted on the basis of the stoichiometry of the mixtures. This finding can be explained by the presence of microscopic configurational inhomogeneity in water-methanol mixtures.     

Atomistic Modeling of Silica Based Sol-Gel Processes

Density Functional Theory is used to study water, methanol, ethanol, TMOS, and TEOS molecules and the most important silica clusters participating in sol-gel processes. Calculated bond lengths, bond angles and electric dipole moments compare well with experimental data. The energy of these molecules is reported and used to discuss the energetics of the hydrolysis and condensation reactions. Molecular Dynamics is employed to simulate liquid water, methanol, ethanol, TMOS, TEOS and experimental sol-gel solutions. Calculated densities and enthalpies of vaporisation compare well with experimental data. Preliminary results are presented for MD simulations of sol-gel solutions.     

Elastic behavior of comb-like polymer chains

<正>Three-dimensional Monte Carlo simulations of comb-like polymer chains with various backbone lengths N_b,arm lengths N_a and arm densities m are carried out to study the elastic behavior of comb-like polymer chains.The radius of gyration,the shape factors and bond length in different cases during elastic process are calculated,and it is found that the comb-like polymer molecules with longer backbone or shorter arm are more close to linear chains.But the arm density m affects the chain conformation non-monotonously.Some thermodynamic properties are also studied.Average Helmholtz free energy and elastic force f all increase with elongation ratioλfor all chains.     

The geometry and electronic structure of the ionic defect in a chain of water molecules between a donor and an acceptor

Quantum chemical calculations of the molecular complexes (NH₃)₃Zn²⁺...(H₂O)_n3...NH₃ (C_n, n=11, 16, 21, and 30) that model the proton donor-aqueous chain-acceptor channel in biological molecules were performed. Periodicity of O-H bond lengths in water chains and charges of the H atoms of H-bonds observed earlier were discussed. In C_n complexes, the geometry and electronic structure of the ionic defect in the aqueous chain with an excess proton were studied. The distributions of O-H bond lengths and charges on H-bond H atoms in the region of the ionic defect obtained in ab initio (B3LYP/6-31+G^**) and semiempirical (PM3) calculations are compared. The influence of aqueous chain extension, the position of the protonated water molecule, and the mobility of water molecules in the chain on the structure of the ionic defect was analyzed.     

Circular hydrogen bond networks on the surface of beta-ribofuranose in aqueous solution

This paper examines the hydration structure on the surface of beta-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of beta-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of beta-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.     

Study of H-bond characteristics in sub- and supercritical methanol

Classical molecular dynamics simulations of various methanol phase lines near the saturation curve and the critical point have been performed to study the changes in H-bonded clusters structure at transition of methanol to supercritical state. Analysis of H-bonds statistics with combined distance-energy H-bond criterion showed that the correlations between topological characteristics of H-bonds and the mole fraction of H-bonded molecules have unique functional representation despite the phase path applied. In the present study, an attempt has been also made to evaluate the degree of hydrogen bonding by combining the DFT computations on classical MD configurations with the natural bond orbital analysis of the waves functions obtained.     

An ab-initio study of the C3H6-HX, C2H4-HX and C2H2-HX hydrogen-bonded complexes with X=F or Cl.

MP2/6-31G** ab-initio molecular orbital calculations have been performed to obtain geometries, H-bond energies and vibrational properties of the C3H6-HX, C2H4-HX and C2H2-HX H-bonded complexes with X=F or Cl. The more pronounced effects on the structural parameters of the isolated molecules due to complexation are verified to the CC and HX bond lengths, which are directly involved in the H-bond formation. They are increased after complexation. The calculated H-bond lengths for the hydrogen complexes for X=F are shorter than those for x-Cl by about 0.55 A, whereas the corresponding experimental value is 0.58 A. The H-bond energies are essentially determined by the nature of the proton donor molecule. For X=F, the AE mean value is 20 kJ/mol, whereas it is approximately 14.5 kJ/mol for X-Cl. The H-bond energies including zero-point corrections show a good correlation with the H-bond lengths. The more pronounced effect on the normal modes of the isolated molecules after complexation occurs to the H-X stretching mode. The H-X stretching frequency is shifted downward, whereas its IR intensity is much enhanced upon H-bond formation. The new vibrational modes arising from complexation show several interesting features.     

Topology of supramolecular structures in ethanol solutions

A quantitative topological analysis of supramolecular structures in ethanol solutions with methanol, propanol, water, benzene, and hexane is performed by the MDGT method previously proposed by the authors. The method is based on a combination of molecular dynamics calculations and the graph theory, which enables the recognition and memorization of supramolecular structures observed in each snapshot of the molecular dynamic trajectory, the averaging of data for any number of these snapshots. Thus, the averaged concentrations of associates (dimers, trimers, etc.) are represented and then the concentrations and characteristics of isomers (e.g., chains, branched chains, rings, etc.), bond lengths, angles, etc. are determined in each group of associates.     

The topological and dynamic characteristics of H-bond networks in water according to computer simulation results

The classic molecular dynamics methods were employed to calculate the topological and dynamic characteristics of H-bond networks in water with the use of various model potentials. The explicit inclusion of specific intermolecular interactions between oxygen and hydrogen atoms additionally stabilized tetrahedrally coordinated molecules and, as a consequence, increased their number in the system. The lifetimes of H-bonds were found to characterize high correlation of movements of nearest environment molecules.     

Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional

Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.     

Cross-polarization with magic-angle spinning kinetics and impedance spectroscopy study of proton mobility,local disorder,and thermal equilibration in hydrogen-bonded poly(methacrylic acid)

The ¹H–¹³C cross-polarization with magic-angle spinning (CP MAS) kinetics was studied in poly(methacrylic acid) (PMAA) having the purpose to track the links between the local order in the main chain and the proton dynamics in peripheral hydrogen bond networks. The experimental CP MAS kinetic curves were analyzed applying the models of isotropic and anisotropic spin-diffusion with thermal equilibration. The fractal dimension D_p ≈ 3 was deduced that indicates that PMAA behaves as an isotropic 3D-system. No proton conductivity in the neat PMAA was deduced from the impedance spectroscopy data analyzing the frequency dependences of the complex dielectric permittivity. The value of local order parameter S = 0.70 for CH₂ in PMAA occupies an intermediate position between 0.63 and 0.85 deduced for CH₂ sites in the main chains of poly(vinyl phosphonic acid) and poly(2-hydroxyethyl methacrylate), that is, the true proton conductor and the polymer that contains the H-bond network, however, no proton conductivity, respectively.     

水溶液中氢键寿命的定义和弛豫机理

氢键弛豫过程决定水溶液中分子的动力学行为,氢键寿命作为理论和实验结果中一个重要的参数通常用以描述溶液中的氢键动力学性质.本文采用SPC/E-P2和SPC/E-OPLS两种力场方法对二甲基亚砜(DMSO)水溶液体系进行分子动力学模拟,计算了四种不同定义下的氢键寿命,并进行了对比阐述,连续性氢键寿命Tc和基于动力学平衡方法下的氢键寿命TR较短,它们忽略了不成功的氢键交换过程,稳定态模型下的氢键寿命TPR能够真实体现氧键转换过程,可作为标度衡量其它量值.间歇性氢键寿命T相对最长,重复统计了氢键成功交换后的恢复概率.随着二甲基亚砜浓度增大,TC、TI、TR和TPR不断增大,分子平动扩散系数在中等浓度达到极小,说明氢键寿命与分子活动性无决定性关联,同类型氢键在不同浓度下的寿命差异表明氢键寿命具有分子环境依赖性;水分子和二甲基亚砜分子氢键个数降低,氢键受激角度扭曲和拉伸概率下降,TC和TR不断接近,氢键交换受体密度降低使氢键交换速率下降,TPR不断增大,氢键寿命与其周围氢键密度密切相关.TI与TPR的比值体现了氢键交换的局域性,其变化趋势与分子平动活动性趋势相同.两种力场下氢键寿命的差异也说明氢键的寿命具有明显的理论模型依赖性.     

Electronic state of small and large cavities for methane hydrate

It is well known that methane hydrate is aggregates of small and large hydrogen bonded water cavities (composed of 12 pentagonal faces of 20 water molecules, and 12 pentagonal and two hexagonal faces of 24 water molecules, respectively) where one methane molecule is encaged. We calculated the methane molecule in vacuum, the small and large cavities by ab initio MO method to clarify the electronic state. The proton of methane in the cavities is shown to form the weak hydrogen bond (O...H[bond]C) between methane and four water molecules, and the H-bond lengths and energies in the small and large cavities were estimated as (0.293 nm, 6.8 kJ/mol) and (0.309 nm, 5.2 kJ/mol), respectively. The calculated values of symmetric C[bond]H stretching frequencies and (13)C-NMR chemical shieldings of the methane in the two cluster cavities show good agreement with the experimental ones observed by Sum et al. and Ripmeester and coworker, respectively.     

Influence of bonded-phase coverage in reversed-phase liquid chromatography via molecular simulation I. Effects on chain conformation and interfacial properties

Particle-based Monte Carlo simulations were employed to examine the effects of bonding density on molecular structure in reversed-phase liquid chromatography. Octadecylsilane stationary phases with five different bonding densities (1.6, 2.3, 2.9, 3.5, and 4.2 mumol/m(2)) in contact with a water/methanol (50/50 mol%) mobile phase were simulated at a temperature of 323 K. The simulations indicate that the alkyl chains become more aligned and form a more uniform alkyl layer as coverage is increased. However, this does not imply that the chains are highly ordered (e.g., all-trans conformation or uniform tilt angle), but rather exhibit a broad distribution of conformations and tilt angles at all bonding densities. At lower densities, significant amounts of the silica surface are exposed leading to an enhanced wetting of the stationary phase. At high densities, the solvent is nearly excluded from the bonded phase and persists only near the residual silanols. An enrichment in the methanol concentration and a disruption in the mobile phase's hydrogen bond network are observed at the interface as bonding density is increased.     

Surface protonation at the rutile (110) interface: explicit incorporation of solvation structure within the refined MUSIC model framework

The detailed solvation structure at the (110) surface of rutile (alpha-TiO2) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 A of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 degrees C that agrees quantitatively with the experimentally determined value (5.4+/-0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pHznpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 degrees C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pHznpcvalue of the rutile (110) surface at 25 degrees C into quantitative agreement with the experimental value (4.8+/-0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 degrees C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite (alpha-SnO2) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.     

Treatment of dilute clusters of methanol and water by ab initio quantum mechanical calculations

Large molecular clusters can be considered as intermediate states between gas and condensed phases, and information about them can help us understand condensed phases. In this paper, ab initio quantum mechanical methods have been used to examine clusters formed of methanol and water molecules. The main goal was to obtain information about the intermolecular interactions and the structure of methanol/water clusters at the molecular level. The large clusters (CH(4)O...(H(2)O)(12) and H(2)O...(CH(4)O)(10)) containing one molecule of one component (methanol or water) and many (12, 10) molecules of the other component were considered. M?ller-Plesset perturbation theory (MP2) was used in the calculations. Several representative cluster geometries were optimized, and nearest-neighbor interaction energies were calculated for the geometries obtained in the first step. The results of the calculations were compared to the available experimental information regarding the liquid methanol/water mixtures and to the molecular dynamics and Monte Carlo simulations, and good agreement was found. For the CH(4)O...(H(2)O)(12) cluster, it was shown that the molecules of water can be subdivided into two classes: (i) H bonded to the central methanol molecule and (ii) not H bonded to the central methanol molecule. As expected, these two classes exhibited striking energy differences. Although they are located almost the same distance from the carbon atom of the central methanol molecule, they possess very different intermolecular interaction energies with the central molecule. The H bonding constitutes a dominant factor in the hydration of methanol in dilute aqueous solutions. For the H(2)O...(CH(4)O)(10) cluster, it was shown that the central molecule of water has almost three H bonds with the methanol molecules; this result differs from those in the literature that concluded that the average number of H bonds between a central water molecule and methanol molecules in dilute solutions of water in methanol is about two, with the water molecules being incorporated into the chains of methanol. In contrast, the present predictions revealed that the central water molecule is not incorporated into a chain of methanol molecules, but it can be the center of several (2-3) chains of methanol molecules. The molecules of methanol, which are not H bonded to the central water molecule, have characteristics similar to those of the methane molecules around a central water molecule in the H(2)O...(CH(4))(10) cluster. The ab initio quantum mechanical methods employed in this paper have provided detailed information about the H bonds in the clusters investigated. In particular, they provided full information about two types of H bonds between water and methanol molecules (in which the water or the methanol molecule is the proton donor), including information about their energies and lengths. The average numbers of the two types of H bonds in the CH(4)O...(H(2)O)(12) and H(2)O...(CH(4)O)(10) clusters have been calculated. Such information could hardly be obtained with the simulation methods.