Direct correlation functions for three-site and four-site water models

ABSTRACT

Direct correlation functions (DCFs) play a pivotal role in modern liquid-state theories and are virtually indispensable for non-mean-field implementation of the classical density functional theory (cDFT). Whereas analytical expressions have been derived for the DCFs of simple fluids and electrolytes, DCFs for molecular systems are attainable only through numerical solution of the integral-equation theories in combination with molecular simulation or an approximate closure. Unlike radial distribution functions, DCFs reflect the variational of the local chemical potential of individual atoms/interaction sites with the density-profile fluctuations, which are difficult to be sampled from the simulation trajectory. This article presents an improved numerical procedure to calculate the DCFs of three-site (SPC/E and TIP3P) and four-site (TIP4P-Ew) water models based on the reference interaction site model and molecular dynamics simulations. In combination with the modified fundamental measure theory for the bridge functionals, the DCFs have been utilised to predict the hydration free energies of 504 small organic molecules. The theoretical predictions yield an average unsigned error of 0.66 kcal/mol in comparison with the simulation data, better than that (～1 kcal/mol) reported in previous cDFT calculations.     

Molecular dynamics simulations of the chiral recognition mechanism for a polysaccharide chiral stationary phase in enantiomeric chromatographic separations

We use explicit-solvent fully atomistic molecular dynamics (MD) simulations, permitting all the interactions between the atoms constituting the polymeric chiral stationary phase (CSP), the solvent molecules and the drug molecule enantiomers, to better understand the chiral recognition mechanism that makes chromatographic separation possible. Using amylose tris(3,5-dimethylphenyl carbamate) (ADMPC) as prototype, three solvent systems, and ten racemates as solutes, we seek a molecular dynamics average quantity that could serve as a metric that predicts which of the two enantiomers will elute first and also correlates with the ratio of retention times for enantiomers. To better understand the molecular dynamic chiral recognition that provides the discrimination which results in the separation of enantiomers by high performance liquid chromatography, we examine the differences in hydrogen bonding lifetimes in various donor–acceptor pairs between the drugs and the ADMPC, and map out the differences in ring-ring interactions between the drugs and the ADMPC. Several MD average quantities related to hydrogen-bonding lifetimes correlate with the ratio of retention times for the enantiomers. One of these quantities provides a prediction of the correct elution order 90% of the time, and the ratios of these quantities for the enantiomers provide linear correlation (0.85 coefficient) with experimental separation factors.     

On the correlation between phonon spectra and surface segregation features in Ag-Cu–Ni ternary nanoalloys

Atomic scale characterization of chemical ordering, compositional distribution and microstructure is of tremendous importance for applications such as catalysis which is primarily dominated by processes occurring at surface and is strongly influenced by the subsurface layers. Phonon spectra obtained from molecular dynamics simulations of single metals as well as their bimetallic and ternary alloy nanoclusters can be used to obtain new insights into the atomic scale distribution in the nanoclusters, their microstructure and dynamical properties. Monte-Carlo (MC) simulations are used to obtain the minimum energy configurations of various Ag–Cu–Ni ternary alloys in which the Ag content is systematically varied from 0 to 50%Ag while keeping the relative composition of Cu and Ni constant. Detailed compositional analyses of the final MC configurations are carried out. The generated microstructure comprised of surface segregated structures in which Ag atoms occupy low coordination sites such as corners, edges and faces. As the Ag content in the ternary alloy is increased, the surface sites get increasingly occupied with the lowest coordination sites being populated first. The Cu and Ni compositions in the interior of the cluster show compositional oscillation. The final alloy microstructure is dictated by the competition between the various entropic and energetic factors. Our analysis of the phonon density of states identifies various surface (low frequency) and bulk (high frequency) modes which is determined by their location in the nanocluster and the local environment. Systematic trends in the observed peak intensities and frequency shifts at the low and high frequency ends of the spectrum for the various alloy compositions are explained on the basis of bond-lengths, local coordination, extent of alloying, and neighboring elemental environment. We find that the characteristic microstructural features observed at the atomic scale are strongly correlated to the vibrational densities of states of the constituent atoms in nanoalloys. Comparisons with experimental investigations are made where possible. Such a characterization method provides a predictive tool for materials which are extremely important for catalytic applications and emerging energy technologies.     

Dynamical and structural properties of adsorbed water molecules at the TiO2 rutile-(110) surface: interfacial hydrogen bonding probed by ab-initio molecular dynamics

ABSTRACT

Ab-initio molecular dynamics (AIMD) simulations have been carried out to study a range of different and energetically-accessible adsorbed-water configurations and motifs for their vibrational and structural characteristics, in contact with rutile-(110) interfaces at 100?K. The radial pair distribution function between the titanium atoms at the interface and the hydrogen and oxygen atoms in the water monolayer show an orientation of the water molecules parallel to the surface of titania, and with hydrogen atoms pointed in the opposite direction to the surface. In some cases, a distinctive vibrational frequency region between 2500 and 3000?cm^?1 has also been observed, due to a strong dispersion interaction between water molecules. This behaviour is also seen in experimental studies of thin-film water coverage on TiO₂ surfaces.     

Cluster-solid interactions: A molecular dynamics investigation

Abstract

The interaction of small energetic clusters of metal atoms with surfaces has been investigated by molecular dynamics computer simulations. A wide variety of cluster-solid combinations have been studied so that the effects of the energy, size, and angle of incidence of the cluster, and the relative elastic properties of the cluster and substrate could be elucidated. ‘Soft landings’ were also investigated. From these studies, a mechanism map for cluster-solid interactions is developed. The results have particular importance for cluster beam deposition of thin films. The simulations are fully dynamical and 3-dimensional; they employ embedded-atom method potentials, which have been modified for interactions at close separations. A scheme for reducing the CPU time that is required for these and other simulations of radiation effects is described.     

Ionization by H+2. Molecular effect

The molecular effect in the ionization of inner shell electrons of aluminum atoms by energetic H⁺₂ molecules has been calculated. We distinguish between the molecular effect in Al and Al₂O₃. We conclude that in the case of Al the protons of the cluster have a definite orientation but in the case of Al₂O₃ the orientation is at random.     

光谱法研究氢等离子体循环机制

利用多道光学分析仪测量Hα线形分布,从线形的分布推出再循环的氢原子主要来源于离子中性化后的反射和氢分子的离解。通过双高斯拟合H_α线形分布,由多普勒频移得出了氢原子的入射速度。从氢原子能量分布上的特征峰得出氢分子的离解方式主要是电离和直接离解。     

Application of z-COSY experiment and its variant for accurate chiral discrimination by 1H NMR

We report the application of z-COSY experiment and a band selected version of it by employing a selective 90° pulse entitled BASE-z-COSY for precise chiral discrimination, quantification of enantiomeric excess and the analyses of the ¹H NMR spectra of chiral molecules aligned in the chiral liquid crystalline solvent poly-γ-benzyl-l-glutamate (PBLG). We have demonstrated their applicability for obtaining very high resolution in the ¹H NMR spectra of small organic molecules. It is well known that the commonly employed z-COSY experiment disentangles the spectral complexity, provides pure phase spectra with high resolution, aids in the complete spectral analyses, in addition to yielding information on relative signs of the couplings. The BASE-z-COSY experiment possesses all these properties, permits the measure of enantiomeric excess, in addition to large saving of instrument time.     

An analysis of the conformers of 1,5-hexadiene

High level theoretical methods have been used to predict the energetic ordering of the conformations of 1,5-hexadiene. Presented are optimized geometries and relative energies for ten energetically distinct conformations of the molecule and two enantiomeric conformations. Previous work had predicted that the gauche (or skew) conformation about the central carbon—carbon bond is the lowest in energy. However, we have found that the conformational energies of 1,5-hexadiene, unlike n-butane, are remarkably similar. We postulate this to be the reason for poor performance (for example, in comparisons with variable temperature NMR studies) of some molecular mechanics simulations on molecules of this type in the past. With the DZP CCSD(T) method, the gauche(120)/anti/gauche(120) conformer is predicted to be the global minimum, followed 0.06kcalmol^?1 higher in energy by the gauche(120)/anti/gauche(?120) structure, followed another 0.03 kcal mol^?1 higher in energy by the gauche(120)/gauche(60)/gauche(?120) arrangement. The three earlier reported molecular mechanics conformational energy surfaces all rise much more steeply from the gauche(120)/anti/gauche(120) and gauche(120)/gauche(60)/gauche(?120) structures.     

Enantioseparation on a chiral nanostructured surface: Effect of molecular shape

In this paper we use the Monte Carlo simulation method to study adsorption of chiral molecules on a solid surface with periodic distribution of active sites. Namely, equilibrium adsorption of a racemic mixture of enantiomers represented by homonuclear tetramers is modeled on a square lattice with a chiral pattern of active sites. We consider two possible chiral structures of the tetramers which differ only by chain geometry but have equal adsorption energies. The effect of the chain geometry on the effectiveness of separation is assessed by comparing the corresponding adsorption selectivities obtained from the simulations. We present results of model calculations in which the parameters do not refer to any particular experimental system. These results indicate that the model chiral surface can, in general, adsorb preferentially the complementary enantiomer, regardless of its chain conformation. Specifically, it was shown that changes in the tetramer geometry, from S-shaped to -shaped, lead to marginal changes in the shape of both single component and mixed adsorption isotherms calculated for the enantioselective surface. In this context, the enantiomer separation on the surface proposed in this work was shown to be insensitive to molecular shape of the adsorbing species.     

Evaluation of the SSC/LHNC,SSCF and PY approximations for short ranged,anisotropic potentials

Three approximations for the orientational correlation function of molecular fluids—the single super chain/linearized hypernetted chain (SSC/LHNC), single super chain f-expansion (SSCF) and Percus-Yevick (PY) approximation—are evaluated in the dense liquid state for a fluid inter-acting with short ranged anisotropic interactions. These interactions are prototypical of the forces that determine the non-spherical shape of symmetric linear molecules. We find that SSC/LHNC is very poor, failing to predict many of the structural features present in the Monte Carlo (MC) simulation results. The PY and SSCF approximations produce much better results; however, neither approximation is completely satisfactory.     

熔融Rb2ZnCl4的分子动力学模拟研究

采用在RbCl模拟和ZnCl₂模拟中选用的两体有效势，进行了晶态和熔融态Rb₂ZnCl₄的分子动力学模拟.模拟给出了Rb₂ZnCl₄ 6种径向分布函数，Zn-Cl和Rb-Cl间径向分布函数与新近的广延X射线吸收精细结构实验结果很好相符.在模拟产生的瞬态构型基础上进行了键序参数分析，研究了晶态和熔融态中的局部结构.模拟结果表明，Zn原子与其近邻Cl原子构成相当稳定的正四面体结构，并且熔融Rb_关键词：     

Sulphur on rutile(1 1 0): A theoretical study

Reactions of elementary sulphur with the rutile (1 1 0) surface are of interest for catalytic desulphurization and have recently been studied experimentally. Here a complete mechanism for the sulphurization of the surface in UHV experiments has been derived from the results of first principles molecular dynamics simulations. It provides the dissociation of S₂ molecules, the reaction of S atoms with oxygen atoms in the surface, the insertion of sulphur atoms into surface vacancies and the formation of SO_x species. Possible elementary steps for these processes are discussed in the paper on the basis of the calculations.     

An analytical theory for diffusion of fluids in crystalline nanoporous materials

An analytical theory for diffusion of fluids in zeolites and other nanoporous materials has been developed. The theory incorporates molecular level information about the nanoporous material, which is obtainable from an energy minimization and does not require molecular dynamics computer simulations. The theory is statistical mechanical in nature and assumes a lattice composed of adsorption sites. The theory yields a self-diffusion coefficient, which is a function of (i) temperature, (ii) adsorbate density, (iii) adsorbate size, (iv) adsorbate-adsorbate energetic interaction and (v) adsorbate-pore energetic interaction. The theory is generalized and is applicable to nanoporous materials with three-dimensional porous networks (e.g. faujusite) and one-dimensional porous networks (e.g. A1P0₄-5).

The theory is self-contained and incorporates no fitting parameters. The theory does not require computational effort beyond a few seconds on a standard personal computer.     

Molecular dynamics simulations on local structure and diffusion in liquid TixAl1−x alloys

The microscopic structure and dynamics of liquid Ti_xAl_1-x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti_0.75Al_0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.     

Plasma-polymerized HMDSO coatings to adjust the silver ion release properties of Ag/polymer nanocomposites

The immobilization of an ad hoc designed chiral imidazolidin-4-one onto iron oxide magnetic nanoparticles (MNPs) is described, to afford MNP-supported MacMillan’s catalyst. Morphological and structural analysis of the materials, during preparation, use, and recycle, has been carried out by transmission electron microscopy. The supported catalyst was tested in the Diels–Alder reaction of cyclopentadiene with cinnamic aldehyde, affording the products in good yields and enantiomeric excesses up to 93 %, comparable to those observed with the non-supported catalyst. Recovery of the chiral catalyst has been successfully performed by simply applying an external magnet to achieve a perfect separation of the MNPs from the reaction product. The recycle of the catalytic system has been also investigated. Noteworthy, this immobilized MacMillan’s catalyst proved to be able to efficiently promote the reaction in pure water.     

Influence of nonlinear atomic interaction on excitation of intrinsic localized modes in carbon nanotubes

Excitation of intrinsic localized modes (ILMs) in carbon nanotubes (CNTs) with different chiral structures was investigated by molecular dynamics simulations. For CNTs with a chiral angle less than or equal to 30^°, energy concentration that continued for more than 200 fs was found in a localized area, where a pair of neighboring atoms strongly oscillated with a higher vibrational frequency than the upper bound of phonon bands. This evidently indicates excitation of the ILM. On the other hand, the ILM was not excited in CNTs with a chiral angle greater than or equal to 41^°. Analyzing the nonlinearity of the interaction between excited atoms in the ILM vibration mode, we elucidated that nonlinearity predominates the selective ILM excitation. Furthermore, stronger nonlinearity excites ILMs with both higher frequency and longer lifetime.     

Fourier transform of the collagen triple-helical structure and its significance

The Fourier transforms of the collagen molecular structure have been calculated taking into consideration various side chain atoms, as well as the presence of bound water molecules. There is no significant change in the calculated intensity distribution on including the side chain atoms of non-imino-acid residues. Taking into account the presence of about two bound water molecules per tripeptide unit, the agreement with the observed x-ray pattern is slightly improved. Fourier transforms have also been calculated for the detailed molecular geometries proposed from other laboratories. It is found that there are no major differences between them, as compared to our structure, either in the positions of peak intensity or in the intensity distribution. Hence it is not possible to judge the relative merits of the various molecular geometries for the collagen triple helix from a comparison of the calculated transforms with the meagre data available from its x-ray fibre pattern. It is also concluded that the collagen molecular structure should be regarded as a somewhat flexible chain structure, capable of adapting itself to the requirements of the different side groups which occur in each local region.     

The method of local fields: A bridge between molecular modelling and dielectric theory

At the nanoscale, the charge distribution in a cluster of several atoms or molecules can be calculated ab initio, i.e. without free parameters. Molecular modelling is limited to a relatively small number of atoms compared to macroscopic materials with myriads of atoms. On the other hand, dielectric and ferroelectric properties of macroscopic matter are described by classical theory using mean-field approximations, e. g. the formula of Clausius–Mossotti for dielectrics and the Landau–Ginzburg–Devonshire theory or rather the molecular field theory by Weiss for ferroelectrics. In the context of multiscale simulations we present a microscopic model for dielectrics and ferroelectrics consisting of discrete atoms and / or dipoles. Parameters calculated from molecular modelling can be used here as input to our simulations in order to calculate bigger systems now. All electrostatic interactions are considered and the electrodes are taken into account using the method of images. Based on thermally activated processes, permanent dipoles fluctuate in double well potentials according to the Boltzmann statistics. Neutral atoms are modelled by induced dipoles having dipole moments proportional to the locally prevailing field. The numerical calculations are based on deterministic local field computations and on weighted probabilistic dynamic Monte Carlo steps.     

“Gold corrosion”: red stains on a gold Austrian Ducat

Femtosecond laser induced adsorption site changes of CO at nanoparticulate palladium aggregates have been investigated using laser light at =400 nm and pulse lengths of 70 fs. The average sizes of the aggregates grown by evaporating palladium atoms onto an epitaxial Al₂O₃ film on NiAl(110) were varied between 100 and 6000 atoms per island. Amorphous aggregates grown at 120 K and crystalline aggregates grown at 300 K have been investigated. Beyond laser-induced migration of CO already reported for nanosecond experiments, adsorbate-induced surface roughening is apparent from Fourier-transform infrared reflection absorption spectroscopy. The laser-induced processes are correlated to the presence of higher local adsorbate densities and a substantial population of edge sites. A model is suggested attributing surface roughening to the formation of local hot spots after coherent electronic excitation via heating through highly vibrationally excited adsorbate states and energetic channelling along chains of elevated local adsorbate densities. The processes are most efficient for intermediate aggregate sizes. In contrast to nanosecond experiments, a few percent of CO molecules are desorbed during the femtosecond experiments from smaller aggregates. PACS 82.53.St