水-甲醇体系的Monte Carlo分子膜拟

本文应用Monte Carlo分子膜拟方法对水、甲醇水-甲醇的1:1混合物、甲醇无限稀释时的水溶液和水无限稀释时的甲醇溶液等五个体系进行了研究。采用TIP分子位能函数, 得到了上述体系的热力学性质、原子径向分布函数、分子氢键配位数分布。并以Monte Carlo分子模拟获得的结构函数与X射线衍射实验结果进行了比较。     

Hydration structure around a non-electrolyte molecule as revealed by monte carlo calculation: have you seen the “iceberg”?

Monte Carlo calculations have been carried out for pure water and an infinitely dilute aqueous solution of methanol at 298.15 K at ordinary density by the Metropolis method in NTV ensemble. The hydration structure around methanol revealed by a graphic display technique indicates a structure-forming effect near the hydrophobic group.     

A theoretical investigation of the enol content of acetic acid and the acetate ion in aqueous solution

Ab initio molecular orbital calculations and statistical Monte Carlo simulations employing a combined quantum and molecular mechanical potential were used to determine the enol contents of acetic acid and the acetate ion in aqueous solution. A pK_E of 19.3 ± 0.3 was predicted for the keto-enol equilibrium of acetic acid, and 21.8 ± 0.8 for the acetate ion in water. The results are found to be in good accord with Guthrie's calculations based on disproportionation reactions and kinetic data. Combining with the experimental pK_a value of acetic acid, we obtained pK_a^k = 26.6 for ionization of acetic acid as a carbon acid in water, and pK_a^E = 7.3 for ionization of the enol of acetic acid.     

Solubility of carbon dioxide in aqueous solutions of methanol. Predictions by molecular simulation and comparison with experimental data

The solubility of carbon dioxide in pure methanol, and in aqueous solutions of methanol, was computed using the Gibbs ensemble Monte Carlo (GEMC) technique for 313, 354, and 395 K at pressures up to 9 MPa. Three solvent mixtures (of methanol and water) with methanol mole fractions of 10, 50, and 75 mole percent (in the gas-free solvent mixture) were studied. The Monte Carlo simulations were conducted in an isothermal-isobaric ensemble applying effective pair potentials for the pure components from literature. Common mixing rules without any adjustable binary interaction parameters were used to describe the interactions between the mixture components. Overall, a good agreement between simulation results and recently published experimental data is achieved.     

Liquid methanol Monte Carlo simulations with a refined potential which includes polarizability, nonadditivity, and intramolecular relaxation

Monte Carlo simulations of liquid methanol were performed using a refined ab initio derived potential which includes polarizability, nonadditivity, and intramolecular relaxation. The results present good agreement between the energetic and structural properties predicted by the model and those predicted by ab initio calculations of methanol clusters and experimental values of gas and condensed phases. The molecular level picture of methanol shows the existence of both rings and linear polymers in the methanol liquid phase.     

A Monte Carlo simulation of Fe2+ aqueous solvation

A Monte Carlo simulation of Fe²⁺ aqueous solvation, at 298 K, including 100 water molecules, has been done using periodic boundary conditions under the minimum image conversion. The energy has been calculated in the pair-potential approach, employing the MCY potential for the H₂OH₂O interaction and an ab initio analytical potential generated by us for the Fe²⁺H₂O interaction. The examination of interaction energies and of the radial distribution functions clearly show that the first hydration shell is formed by eight water molecules. By classifying the generated configurations into different significant structures of the solvent, it has been found that the eight water molecules of the first hydration shell are situated in a lightly distorted D_4d structure which maximizes the water—solute stabilization and minimizes the water—water repulsion. Finally, the validity of our theoretical predictions is discussed.     

Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations

Many structural models for the stationary phase in reversed-phase liquid chromatography (RPLC) systems have been suggested from thermodynamic and spectroscopic measurements and theoretical considerations. To provide a molecular picture of chain conformation and solvent partitioning in a typical RPLC system, a particle-based Monte Carlo simulation study is undertaken for a dimethyl octadecyl (C(18)) bonded stationary phase on a model siliceous substrate in contact with mobile phases having different methanol/water concentrations. Following upon previous simulations for gas-liquid chromatography and liquid-liquid phase equilibria, the simulations are conducted using the configurational-bias Monte Carlo method in the Gibbs ensemble and the transferable potentials for phase equilibria force field. The simulations are performed for a chain surface density of 2.9 micromol/m(2), which is a typical bonded-phase coverage for mono-functional alkyl silanes. The solvent concentrations used here are pure water, approximately 33 and 67% mole fraction of methanol and pure methanol. The simulations show that the chain conformation depends only weakly on the solvent composition. Most chains are conformationally disordered and tilt away from the substrate normal. The interfacial width increases with increasing methanol content and, for mixtures, the solvent shows an enhancement of the methanol concentration in a 10 Angstrom region outside the Gibbs dividing surface. Residual surface silanol groups are found to provide hydrogen bonding sites that lead to the formation of substrate bound water and methanol clusters, including bridging clusters that penetrate from the solvent/chain interfacial region all the way to the silica surface.     

Relative log P and solution structure for small organic solutes in the chloroform/water system using monte carlo methods

Relative log P values of dimethylether to methanol and dimethylamine to methylamine were calculated in the chloroform/water system using Monte Carlo simulations and statistical perturbation theory. Correct ordering of the calculated relative log Ps was obtained for the two pairs although the method leads to an overestimation of these values. In aqueous solution, both dimethyl ether and dimethylamine solutes are proton acceptors forming a single hydrogen bond to water. Dimethylamine forms a stable N? H-Ow hydrogen bond while the water hydrogen is poorly localized in the O? H-Ow bond to the ether. In chloroform, the solvent molecules are less ordered around the solutes than was found around methanol and methylamine.     

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic ligands: Monte Carlo simulations results

We report results of the Monte Carlo simulations of systems containing heterodimers of biological active ligands and water molecules. The study was designed to identify the possible formation of intermolecular hydrogen bonds in such systems in order to investigate the molecular mechanisms of hetero-association of aromatic ligands in aqueous solution. The geometry optimization and the calculation of the atomic charges of free ligands were carried out at DFT/B3LYP level of theory. Monte Carlo simulations with Metropolis algorithm were used to determine the low energy conformations of heterodimers in water clusters. The analysis of the Monte Carlo simulation results allows us to describe in detail the hydration properties of all investigated heterodimers and to determine the intermolecular hydrogen bonds between the functional donor–acceptor groups for some of hetero-associates under investigation. In the case of heterodimers without intermolecular hydrogen bonds, the additional stabilization of these hetero-complexes can be explained by the formation the water bridges between donor and acceptor groups of the ligands.     

Simulating fluid-phase equilibria of water from first principles

Efficient Monte Carlo algorithms and a mixed-basis set electronic structure program were used to compute from first principles the vapor-liquid coexistence curve of water. A water representation based on the Becke-Lee-Yang-Parr exchange and correlation functionals yields a saturated liquid density of 900 kg/m3 at 323 K and normal boiling and critical temperatures of 350 and 550 K, respectively. An analysis of the structural and electronic properties of the saturated liquid phase shows an increase of the asymmetry of the local hydrogen-bonded structure despite the persistence of a 4-fold coordination and decreases of the molecular dipole moment and of the spread of the lowest unoccupied molecular orbital with increasing temperature.     

Molecular simulation with variable protonation states at constant pH

A new method is presented for performing molecular simulations at constant pH. The method is a Monte Carlo procedure where trial moves consist of relatively short molecular dynamics trajectories, using a time-dependent potential energy that interpolates between the old and new protonation states. Conformations and protonation states are sampled from the correct statistical ensemble independent of the trial-move trajectory length, which may be adjusted to optimize efficiency. Because moves are not instantaneous, the method does not require the use of a continuum solvation model. It should also be useful in describing buried titratable groups that are not directly exposed to solvent, but have strong interactions with neighboring hydrogen bond partners. The feasibility of the method is demonstrated for a simple test case: constant-pH simulations of acetic acid in aqueous solution with an explicit representation of water molecules.     

Molecular simulation study on adsorption of methanol/water mixtures in mesoporous silicas modified pore surface silylation

Two types of molecular simulation techniques have been utilized to investigate adsorption of methanol/water mixtures in a mesoporous silica with a hydrophobic pore surface: the NVT-ensemble Molecular Dynamics method with the melt-quench algorithm for modeling a fully-silylated mesoporous silica and the μVT-ensemble Orientaional-Biased Monte Carlo method for calculating adsorption isotherms. Adsorption isotherms of methanol and water at 333 K are calculated for an equi-relative-pressure mixture (each component has the same relative pressure which is defined as the ratio of the partial pressure to the saturation pressure of the pure gas) together with pure gases. In the case of the pure gas, water hardly adsorb even at elevated pressures, while the adsorption isotherm for methanol shows the condensable adsorption. On the other hand, in the case of the mixture, water molecules are substantially adsorbed along with methanol molecules, showing an isotherm representing the condensation mechanism. In addition, it is found that the separation factor of methanol to water is the highest in the case of monolayer adsorption from a liquid mixture.     

The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents

A simple strategy to compose a new all-atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (E(TOTAL)) is divided into three components; a single amino acid potential term (E(SAAP)), an interamino acid nonbonded interaction term (E(INTER)), and a miscellaneous term (E(OTHERS)), which is ignored (or considered to be constant) at the current version of the force field. The E(INTER) term consists of electrostatic interactions (E(ES')) and van der Waals interactions (E(LJ')). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of For-Ala(2)-NH(2) in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for For-Gly(10)-NH(2) and For-Ala(10)-NH(2) showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (E(TOTAL)) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the E(SAAP) term) may play definitive roles on the topologies of protein secondary structures.     

Structure of the liquid-vapor interface of water-methanol mixtures as seen from Monte Carlo simulations

Monte Carlo simulation of the vapor-liquid interface of water-methanol mixtures of different compositions, ranging from pure water to pure methanol, have been performed on the canonical (N, V, T) ensemble at 298 K. The analysis of the systems simulated has revealed that the interface is characterized by a double layer structure: methanol is strongly adsorbed at the vapor side of the interface, whereas this adsorption layer is followed at its liquid side by a depletion layer of methanol of lower concentration than in the bulk liquid phase of the system. The dominant feature of the interface has been found to be the adsorption layer in systems of methanol mole fractions below 0.2, and the depletion layer in systems of methanol mole fractions between 0.25 and 0.5. The orientation of the molecules located at the depletion layer is found to be already uncorrelated with the interface, whereas the methanol molecules of the adsorption layer prefer to align perpendicular to the interface, pointing straight toward the vapor phase by their methyl group. Although both the preference of the molecular plane for a perpendicular alignment with the interface and the preference of the methyl group for pointing straight to the vapor phase are found to be rather weak, the preference of the methyl group for pointing as straight toward the vapor phase as possible within the constraint imposed by the orientation of the molecular plane is found to be fairly strong. One of the two preferred orientations of the interfacial water molecules present in the neat system is found to disappear in the presence of methanol, because methanol molecules aligned in their preferred orientation can replace these water molecules in the hydrogen-bonding pattern of the interface.     

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.     

Effective interaction energy of water dimer at room temperature: an experimental and theoretical study

Buffer-gas pressure broadening for the nu(1)+nu(3) band of H(2)O at 1.34-1.44 mum for a variety of buffer gases was investigated at room temperature using continuous-wave cavity ring-down spectroscopy. The effective interaction energy of water dimer under room temperature conditions was evaluated from the pressure broadening coefficients for rare gases using Permenter-Seaver's relation. Monte Carlo simulations were performed using ab initio molecular orbital calculations to evaluate the interaction energies for the water dimer at 300 K. In this theoretical calculation, the orientations of the two water molecules were statistically treated.     

Influence of the size of fixed-rigidity spheres on the structural and energy characteristics of hydrophobic hydration

Monte Carlo simulations of molecular configurations of aqueous solutions of spherical particles with a special potential of solute—water interaction were carried out. The influence of the particle size on the properties of hydration shells was investigated. Two regimes of hydrophobic hydration with a crossover point at 0.4 nm were found. Hydration of smaller particles causes insignificant changes in the properties of water. Particles larger than 0.4 nm break the liquid water structure. Breaking effects are more pronounced in the first hydration shell of particles. Dewetting of hard sphere surfaces predicted by the LCW phenomenological theory has peculiarities in the case of hydration of fixed-rigidity spheres. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1777–1786, September, 2008.     

A new form for intermolecular potential energy functions

A new intermolecular potential energy function is presented for Monte Carlo and molecular dynamics simulations of liquids, solutions and other molecular assemblies. The potential energy function is expressed in terms of intermolecular overlap integrals over localized molecular orbitais of isolated molecules and Coulomb potentials between fractional point charges placed on the nuclei. The potential function is easy to generate and is applicable to a wide range of molecules. As examples the potential functions are generated for the water, ammonia and hydrogen fluoride dimers.     

The Kohn-Sham density of states and band gap of water: from small clusters to liquid water

Electronic properties of water clusters (H2O)(n), with n=2, 4, 8, 10, 15, 20, and 30 molecules were investigated by sequential Monte Carlo/density-functional theory (DFT) calculations. DFT calculations were carried out over uncorrelated configurations generated by Monte Carlo simulations of liquid water with a reparametrized exchange-correlation functional that reproduces the experimental information on the electronic properties (first ionization energy and highest occupied molecular orbital-lowest unoccupied molecular orbital gap) of the water dimer. The dependence of electronic properties on the cluster size (n) shows that the density of states (DOS) of small water clusters (n>10) exhibits the same basic features that are typical of larger aggregates, such as the mixing of the 3a1 and 1b1 valence bands. When long-ranged polarization effects are taken into account by the introduction of embedding charges, the DOS associated with 3a1 orbitals is significantly enhanced. In agreement with valence-band photoelectron spectra of liquid water, the 1b1, 3a1, and 1b2 electron binding energies in water aggregates are redshifted by approximately 1 eV relative to the isolated molecule. By extrapolating the results for larger clusters the threshold energy for photoelectron emission is 9.6+/-0.15 eV (free clusters) and 10.58+/-0.10 eV (embedded clusters). Our results for the electron affinity (V0=-0.17+/-0.05 eV) and adiabatic band gap (E(G,Ad)=6.83+/-0.05 eV) of liquid water are in excellent agreement with recent information from theoretical and experimental works.