磷酸二氢铵水溶液构型能删和径向分布函数的分子动力学模拟

采用分子动力学模拟对不同温度下磷酸二氢铵水溶液的构型能和径向分布函数进行了研究．磷酸二氢根被看作七节点模型,铵离子被看作五节点模型,而水分子则被看作简单点电荷模型．在饱和温度附近,体系局域粒子数密度有波动．373-400K的溶液势能增长缓慢表明磷酸二氧铵部分分解．磷酸二氢根中的氧原子与铵离子中氢原子的径向分布函数在三种不同温度下呈现明显不同,表明溶液中平均氢键数目随温度的变化明显改变．温度对磷酸二氢根中的氧原子和氧原子的结合有一定的影响,而在饱和溶液中有更多的生长基无产生．     

The structure of liquid N-methyl pyrrolidone probed by x-ray scattering and molecular simulations

The structural properties of liquid N-methyl pyrrolidone have been investigated by combining energy dispersive x-ray diffraction experiments and molecular dynamics simulations with generalized AMBER force field. A very good agreement between theoretical and experimental diffraction patterns was achieved. The analysis of the radial distribution functions shows that the methyl-carbonyl H-bond network observed in the crystal structure is partly preserved in the liquid structure.     

Structure of aqueous sodium metaborate solutions: X-ray diffraction study

A structural analysis of aqueous sodium metaborate solutions (NaBo₂ · nH₂O, n = 10, 15, 20) at 298 ± 0.5 K by a rapid liquid ??-?? X-ray diffractometry with a highly effective X??celerator detector is reported in present paper. The radial distribution functions (RDF) and theoretical partial radial distribution functions for B-O, O-O, Na-O, Na-B, and Na-Na atom pairs were obtained from precisely diffraction data processing. Structure of aqueous sodium metaborate solutions was given through model calculation and described in three different items: hydrated sodium ion, hydrated metaborate ion and ion association. Effects of concentration on the structure of the solutions were discussed in detail. The mechanisms of ion aggregation and the formation of crystal nuclei in the solution are proposed. The results show that a clear picture of the structure of aqueous sodium metaborate solution has been acquired.     

The properties and behavior of supermolecular formations in aging aqueous poly (vinyl alcohol) solutions

The structure of supermolecular formations and the interparticle interaction in aqueous poly(vinyl alcohol) solutions aging at different concentrations were investigated. Integral light scattering was used to determine the single particle scattering functionP(K), the structure functionS(K), and hence the radial distribution functiong(r). Nonrandom arrangement of the supermolecular formations in solutions under study is much less intensive than that of particles in polymer latices.     

Structural properties of liquidN-methylformamide

Monte Carlo simulation of liquidN-methylformamide was carried out at 298 K. The atom-atom spatial distribution functions, concentrations of closed cycles of H-bonds, radial distribution functions of geometric centers of the cycles, and other characteristics of the system of hydrogen bonds and the network built of the lines connecting neighboring molecules were calculated. The effects of electrostatic and van der Waals interactions as well as molecular conformations on the regularities of mutual arrangement of the molecules were investigated. It was found that open chains of H-bonds dominate over closed cycles. Spatial structure of liquidN0methylformamide is determined by packing of the molecules and steric factors and is close to the structure of a random closely packed system of soft spheres. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 235–247, February, 2000.     

Raman spectra of complexes of HCl with DMF with a strong quasisymmetric H-bond in solutions

Raman spectra of complexes of HCl with DMF with a strong quasisymmetric H-bond in solutions were obtained. The formation of these complexes is accompanied by significant changes in almost all the vibration frequencies and line intensities, the changes in Raman and IR spectra being similar in many features. A weak background scattering was found in the Raman spectra, which coincides in shape with the continuous absorption in IR spectra.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1593–1595, September, 1994.This work was supported by the Russian Foundation for Basic Research (Project No. 93-03-18856).     

Hulthén and slater type 2d functions in some excited configurations of sulphur and phosphorus

It is shown that a substantial energy improvement is gained by the variational use of Hulthén orbitals, instead of single Slater orbitals, in the 3d shells of some excited configurations of sulphur and phosphorus. The energies obtained are close to those attained with two-term Slater functions. In some cases the radial distribution functions from Hulthén orbitals are as good an approximation of SCF radial distributions as those from two-term Slater orbitals. Single term 2d functions with only one parameter are found to give almost identical energies and radial distribution functions as those obtained from two-parameter Hulthén orbitals. It is shown that the relationship between one-term 2d orbitals and Hulthén orbitals gives a method of enforcing nuclear cusp conditions on the former with little effect on the energy.     

A simple method for evaluation of the self-consistency of the radial distribution functions and the orientation of water molecules in the first coordination sphere from the results of molecular dynamics calculations

A simple method for determination of the angular orientation of water molecules in the first coordination sphere from the radial distribution functions is proposed. A comparative analysis of the ability of the model potentials of pair interaction to take into account the effects of manybody interactions (MBI) was performed. The responses of the model pair potentials to the MBI effects in the first and second coordination spheres were found to be poorly correlated with each other. It was concluded that it is necessary to derive a new analytical type of potential functions of pair interaction. Published inIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 11, pp. 1842–1846. November. 2000.     

The nature and energy characteristics of intramolecular hydrogen bonds in crystals

The review concerns the results of systematic X-ray diffraction studies of the electron density distribution in the crystals of compounds with strong intramolecular hydrogen bonds N-H...O, O-H...O, O-H...N, and N-H...S. The advantages of the topological analysis of the electron density distribution function in the analysis of the nature and estimation of the H-bond energies directly from experimental data are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–14, January, 2006.     

过饱和五硼酸钠溶液结构

用快速X射线衍射法测量了298和323K时过饱和五硼酸钠溶液的时间空间平均结构,得到了溶液径向分布函数.通过模型设计及理论计算获得了B-B、B-O、O-O、Na-O、Na-B原子对相互作用的理论偏径向分布函数,并讨论了浓度和温度对五硼酸钠溶液结构的影响.在五硼酸钠过饱和溶液中六水合Na+形成八面体结构,其平均配位数随浓度和温度变化不大,作用距离随温度升高及浓度减小而减小;给出了溶液中主要硼酸盐离子B3O3(OH)4-、B5O6(OH)4-和B(OH)3的水合结构,较高温度及较高浓度有利于更高聚合的多聚硼酸根离子的形成;浓度对硼酸盐离子的第一水合层的水合数影响较大,在较浓的五硼酸钠过饱和溶液中,五硼酸根离子的一个端氧单齿配位到Na+上形成离子对,Na-B特征距离为0.328nm.     

Structural properties of liquid formamide

Computer simulations of liquid formamide were carried out by the Monte Carlo method at 298 and 348 K. The atom-atom spatial distribution functions, the concentrations of closed H-bonded ring, the radial distributions functions of the geometric centers of the rings, and a number of other characteristics of hydrogen-bonded systems were calculated. It was found that the open chains dominate over cyclic structures, which are prone to association and formation of structural heterogeneities. Characteristic types of molecular associates were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1911–1917, October, 1998.     

Structural properties of liquid water

Monte Carlo simulations of molecular configurations of liquid water in theNVT-ensemble atT=298 K using unit cells containing 125 and 1000 molecules were, carried out. Comparison of experimental and calculated radial distribution functions suggests the existence of two types of spatial ordering in water. Structural properties of low-energy molecular clusters and associates of closed cycles of H-bonds were determined. The properties of the network of H-bonds can be described by a set of fundamental constants and one free parameter,viz., the probability of bond formation. The existence of long-range correlations in spatial arrangement of both the molecules and the cycles of bonds was established. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 841–851, May, 1999.     

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE‐rich solutions have stronger TFE–water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF₃ groups. The distribution of cluster sizes in solution supports these conclusions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

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.     

The determination of the limiting partial molar volume of solutions of monocarboxylic acids in benzene by molecular dynamics simulation

A molecular dynamics simulation of the limiting solutions of monocarboxylic acids (oleic, stearic, and myristic) in benzene was performed. The radial distribution functions between benzene and dissolved acid atoms were obtained. The functions were used to calculate the limiting partial molar volumes of solutions of the acids. The results were compared with the experimental limiting molar partial volumes of solutions of the acids obtained by precision vibrational densimetry and small-angle neutron scattering.     

Molecular dynamic study of the anomalous behavior of heat capacity in a methanol-water mixture

The molecular dynamic (MD) method is used to study the anomalous behavior of heat capacity in the range of small concentrations of methanol-water solutions. The behavior of the concentration dependence of heat capacity as calculated by the MD method qualitatively coincides with the experimental values. The calculation of contributions from different types of interaction to heat capacity showed that the greatest contribution is made by the interaction between the methanol molecules. The reason for the anomalous behavior of heat capacity is discussed based on the calculation of the mean force potential, radial distribution functions, and hydrogen bond network parameters. Translated fromZhurnal Strukturnoi Khimii, Vol.40, No. 2, pp. 304–313, March–April, 1999.     

Parameters of models and conditional sensitivity coefficients of radial distribution functions for water calculated by molecular dynamics data

The influence of parameters of rigid models of the 12-6-1 type on the properties calculated in computer experiments, viz., radial distribution functions and internal energy, was studied by the method of step-by-step transform of the water models supplemented by calculations of conditional sensitivity coefficients.     

Carbohydrate clustering in aqueous solutions and the dynamics of confined water

We use molecular dynamics simulations to investigate structure and dynamics of fructose aqueous solutions in the 1-5 M concentration range at ambient conditions. We analyze hydration structures, H-bond statistics, and size distribution of H-bonded carbohydrate clusters as functions of concentration. We find that the local tetrahedral order of water is reasonably well-preserved and that the solute tends to appear as scattered "isolated" molecules at low concentrations and as H-bonded clusters for less diluted solutions. The sugar cluster size distribution exhibits a sharp transition to a percolated cluster between 3.5 and 3.8 M. The percolated cluster forms an intertwined network of H-bonded saccharides that imprisons water. For the dynamics, we find good agreement between simulation and available experimental results for the self-diffusion coefficients. Water librational dynamics is little affected by sugar concentration, whereas reorientational relaxation is described by a concentration-independent bulk-like component attributed to noninterfacial water molecules and a slower component (strongly concentration dependent) that arises from interfacial solvent molecules and, hence, depends on the dynamics of the cluster structure itself. Analysis of H-bonding survival probability functions indicates that the formation of carbohydrate clusters upon increasing concentration enhances the H-bond relaxation time and slows down the entire system dynamics. We find that multiexponential or stretched-exponential fits alone cannot describe the H-bond survival probabilities for the entire postlibrational time span of our data (0.1-100 ps), as opposed to a combined stretched-plus-biexponential function, which provides excellent fits. Our results suggest that water dynamics in concentrated fructose solutions resembles in many ways that of protein hydration water.     

Structural peculiarities and the possibility of the existence of small water cluster anions (H2O) n − withn≤4

Structures of (H₂O) _n ⁻ anions withn≤4 were optimized at the UHF/4-31++G^** level and their stability was estimated at the MP2/4-31++G^** level. The trimer anion has a chain-like structure while the tetramer anion can exist either in a chain-like or a cyclic configuration. In the dimer anion and in the chain-like anions, the excess electron density is localized on the terminal water molecule, an acceptor of the H-bond proton. In the cyclic anion, it is uniformly distributed over the free hydrogen atoms. All considered anions have energy values higher than those of the corresponding neutral oligomers. The detachment of an electron from the anions should proceed with the liberation of energy. However, trimer and larger anions are stable against dissociation into individual water molecules and a free electron. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 41–46, January, 1997.