The equivalent potential of water molecules for electronic structure of alanine

Using ab initio calculations based on density functional theory, an equivalent potential of water molecules for the electronic structure of Ala in solution has been obtained. The calculation process consists of three steps: first, the geometric structure of Ala + nH₂O system is determined by searching for the lowest energy of the system using free cluster calculation method. Second, based on the geometric structure obtained, the electronic structure of Ala with the potential of water molecules is calculated using a self-consistent cluster-embedding method. Finally, after replacing water molecules with dipoles, the electronic structure of Ala with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Ala with the potential of dipoles is close to that of water molecules. The calculated results show that the main effect of water molecules is to raise the state for methyl CH₃ by about 0.14 Ry, raising all other eigenvalues by about 0.059 Ry, and widening the energy gap by about 25%. In contrast, the replacement of water molecules by dipoles is comparatively efficient, showing that the effect of water molecules on the electronic structure of Ala can be simulated by a dipole potential, which would be a shortcut calculation.     

The equivalent dipole potential of water for the electronic structure of threonine

The equivalent potential of water for the electronic structure of threonine (Thr) in solution is constructed by the first-principles, all-electrons, ab initio calculations. The main process of calculation consists of three steps. First, the geometric structure of the cluster containing Thr and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Thr with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Thr with the potential of dipoles is calculated. The results show that the major effect of water on the electronic structure of Thr is to raise the occupied molecular orbitals near the Fermi level by about 0.01 Ry on average, and its energy gap is almost not changed. The effect of water on the electronic structure of Thr can be simulated by dipoles potential.     

The equivalent potential of water molecules for electronic structure of cysteine

In order to get more reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. The first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of Cys. The process consists of three steps. First, the electronic structure of the cluster containing Cys and water molecules is calculated. Then, based on the structure, the electronic structure of Cys with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Cys with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Cys with the potential of dipoles is close to that of water molecules. The calculations show that the major effect of water molecules on Cys' electronic structure is lowering the occupied electronic states by about 0.032 Ry, and broadening energy gap by 16%. The effect of water molecules on the electronic structure of Cys can be simulated by dipoles potential.     

The equivalent potential of water molecules for electronic structure of lysine

In order to get more reliable electronic structures of proteins in aqueous solution, it is necessary to construct a potential of water molecules for protein’s electronic structure calculation. The lysine is a hydrophilic amino acid. It is positively charged (Lys+) in neutral water solution. The first-principles, all-electron, ab initio calcula-tions, based on the density functional theory, have been performed to construct such an equivalent potential of water molecules for lysine (Lys+). The process consists of three parts. First, the electronic structure of the cluster containing Lys+ and water molecules is calculated. By adjusting the positions of water molecules, the geometric structure of the cluster having minimum total energy is determined. Then, based on the structure, the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of Lys+ with the potential of dipoles is calculated. The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained. The major effect of water molecules on lysine’s electronic structure is raising the occupied eigenvalues about 0.5032 eV, and broadening energy gap 89%. The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.     

Water behavior in the neighborhood of hydrophilic and hydrophobic membranes: Lessons from molecular dynamics simulations

The study of properties of water in the vicinity of surfaces poses a fascinating challenge. In this article we studied the behavior of water molecules in the neighborhood of membranes. We addressed the question of how these water molecules are influenced by the membranes’ hydrophilicity. Three systems were studied through molecular dynamics simulations: water in the presence of a hydrophilic membrane (PL), water in the presence of a hydrophobic (PB) one and water in the absence of membranes (BULK). Additionally, in order to study the dependence of the effect of the membrane on the behavior of neighboring water molecules with temperature, each system was simulated at three different temperatures (K): 250, 300 and 350. For each condition, kinetic and structural features were studied. The first feature involved the calculation of diffusion coefficients and activation energy. The second feature was evaluated through the study of water density and hydrogen bond distribution. From the present study we concluded that: (1) density studies underestimate the influence of both hydrophilic and hydrophobic membranes on the neighboring water molecules; (2) the hydrophilic and hydrophobic membranes disturb the hydrogen bond network within distances ranging from 1 to 8 nm, depending on the nature of the membrane and the temperature conditions; (3) the presence of a hydrophobic surface results in an enhancement of the natural hydrogen bond network present in liquid water, to a greater extent than what even an ordered Ih ice structure is able to achieve (i.e. PL membrane); (4) the structural enhancement due to the presence of a hydrophobic surface involves roughly 18 to 24 water hydration layers, for ambient and above temperature conditions.     

Simulation of water potential for the electronic structureof serine

First-principles, all-electron, \textit{ab initio} calculations have been performed to construct an equivalent water potential for the electronic structure of serine (Ser) in solution. The calculation is composed of three steps. The first step is to search for the configuration of the Ser + NH₂O system with a minimum energy. The second step is to calculate the electronic structure of Ser with the water molecule potential via the self-consistent cluster-embedding method (SCCE), based on the result obtained in the first step. The last step is to calculate the electronic structure of Ser with the dipole potential after replacing the water molecules with dipoles. The results show that the occupied states of Ser are raised by about 0.017~Ry on average due to the effect of water. The water effect can be successfully simulated by using the dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method.     

Layered lattice gas model for the metal-electrolyte interface

Several models of the diffuse double layer in liquid electrolytes are discussed. These models all involve partitioning the space charge region into a number of planar layers parallel to the metal electrode, with ionic liquid lattice gas, as opposed to idea gas, response in each layer. Each layer may contain both ions and solvent molecules. Several difficulties implicit in the earlier work of Liu on such a model are pointed out. These problems seem to have caused the appearance of an initial charge-free region in Liu's results. A layer model involving Liu's original assumptions of point ionic charges and point dipoles is discussed in detail and is shown to be electrostatically inconsistent. It is replaced by a layer model in which ionic charge resides on each basic layer, with each such layer surrounded symmetrically by charge layers representing the effect of finite-extent permanent dipoles. This model leads, as it should, to Gouy-Chapman behavior in the continuum limit. Finally, a method of including ion hydration effects explicitly in such a model is proposed.     

Finite size effect of ions and dipoles close to charged interfaces

The modified dipolar Poisson-Boltzmann(MDPB) equation,where the electrostatics of the dipolar interactions of solvent molecules and also the finite size effects of ions and dipolar solvent molecules are explicitly taken into account on a mean-field level,is studied numerically for a two-plate system with oppositely charged surfaces.The MDPB equation is solved numerically,using the nonlinear Multigrid method,for one-dimensional finite volume meshes.For a high enough surface charge density,numerical results of the MDPB equation reveal that the effective dielectric constant decreases with the increase of the surface charge density.Furthermore,increasing the salt concentration leads to the decrease of the effective dielectric constant close to the charged surfaces.This decrease of the effective dielectric constant with the surface charge density is opposite to the trend from the dipolar Poisson-Boltzmann(DPB) equation.This seemingly inconsistent result is due to the fact that the mean-field approach breaks down in such highly charged systems where the counterions and dipoles are strongly attracted to the charged surfaces and form a quasi two-dimensional layer.In the weak-coupling regime with the electrostatic coupling parameter(the ratio of Bjerrum length to Gouy-Chapman length) Ξ 1,where the MDPB equation works,the effective dielectric constant is independent of the distance from the charged surfaces and there is no accumulation of dipoles near the charged surfaces.Therefore,there are no physical and computational advantages for the MDPB equation over the modified Poisson-Boltzmann(MPB) equation where the effect of dipolar interactions of solvent dipoles is implicitly taken into account in the renormalised dielectric constant.     

Crystallisation of ice in charged Pt nanochannel

Using molecular dynamics simulations, we examine the crystallisation process of the extended simple point charge model (SPC/E) water confined in a charged Pt nanochannel. The presence of the external electric field enhances the surface layering of water and promotes the super-cooled water to crystallise into Ic ice within tens of nanoseconds. Ic ice is found to nucleate from the interior of the water lamina, and the Pt(111) surfaces do not show a remarkable promotion of Ic ice nucleation. Structural analysis reveals that a two-dimensional hydrogen-bond network is built among the water molecules absorbed on the charged Pt surfaces, which influences the bonding of the molecules between the first and the second layers, and disturbs the formation of tetrahedral structures that match Ic ice, finally resulting in the nucleation-free near the walls. Such arrangements of water molecules remain in the subsequent growth of Ic ice and cause the slowdown of growth velocity while approaching surfaces.     

Ordering of molecular dipole moments in a nanosized water cluster

A water cluster of 1000 molecules is simulated using the method of classical molecular dynamics. The calculation is performed for the “flexible” version of the TIP4P interaction potential for a constant cluster temperature of 180 K. It is found that clusters with a solid crystalline or amorphous core and a liquid-like shell are stable structures. The ferroelectric ordering of the molecular dipole moments in the central part of the cluster is found for both cluster types; this ordering is responsible for a large total dipole moment of these molecular groups. However, this effect is compensated by dipoles in the peripheral cluster layers, so that in general, the mean dipole moment of a cluster appears to be much smaller than that in the case of the random orientation of the cluster molecules.     

Trapping excess electrons in molecular charge pockets on surfaces

This work considers the use of theoretical ab initio calculations to design a novel molecular trap for excess electrons. The basic principle is to develop a model by which these electrons can be stabilized by charge pockets on the surface of molecules. Calculations reveal that systems with OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), while the hydrogen atoms on the opposite side of this surface form a pocket of positive charge that attracts the extra negative charge.     

Simulation of the interface of (1 0 0) rutile with aqueous ionic solution

The interface of the rutile (1 0 0) surface with NaCl solutions has been simulated by classical molecular dynamics. In contrast to earlier simulations the protonation and hydroxylation equilibriums have been adjusted for different pH values (4, 7.4, and 9). The short range order close to the surface is described by two water layers with some orientational order and intermediate layers of positive or negative ions depending on the surface charge. A Stern model is confirmed with a dense layer of counterions on the charged TiO₂ surface and a diffuse layer, which only consists of few ions in our system. The increase of orientational order of the water molecules close to the surface is described by an exponential function with a decay parameter of 1.9 Å, superposed by a damped oscillation which is independent of the pH value. The diffusion is significantly slower than in the bulk within a range of 13 Å from the surface. We propose a common approach for describing the different z-dependences of orientational order and of the diffusion coefficients.     

Computer simulation of the hydrophobic hydration of concave surfaces

Hemispherical objects of radius from 6.5 to 12.2 Å were constructed from tessellated icosahedra where the vertices were hydrophobic ‘atoms’. These hemispheres were hydrated in a periodic box of water and molecular dynamics simulations in the NVE ensemble were performed on this solution at 320K. Results show that water molecules in the concave region exhibit a layered structure and have their dipoles preferentially oriented approximately orthogonal to the radial direction of the hemisphere. They possess fewer hydrogen bonds and near neighbours. Changes in the translational dynamics of these water molecules are not detected, but there is an acceleration of the re-orientational dynamics. This work thus represents the first systematic study of the hydration of concave hydrophobic surfaces.     

Molecular simulation of sodium butyl benzene sulfonate at air–water interface and in aqueous solution

Molecular mechanics(MM) calculations for interfacial behaviour of sodium n-butyl benzene sulfonate (NaNBBS), sodium iso-butyl benzene sulfonate (NaIBBS) and sodium tert-butyl benzene sulfonate (NaTBBS) show a significant effect of the butyl group geometry on the surface area occupied by these molecules at the air–water interface. NaNBBS, in comparison with NaIBBS and NaTBBS, shows a closer molecular packing at the interface. The simulation predicts minimum hydrotrope concentration of each hydrotrope to reach surface saturation and molecular surface area at the interface match with good accuracy. The shape, size and charge of the hydrotrope aggregates obtained by molecular dynamics simulation also match well with the results of small angle neutron scattering experiments on the same hydrotrope. The simulation shows non-regular and ellipsoidal hydrotropes aggregates with substantial charge on the surface. The aggregates are also more open structures as compared to surfactant micelles. The water accessible surface area of a NaNBBS aggregate was 25% lower in comparison to that of NaTBBS aggregate, indicating closer packing of NaNBBS molecules. The fractional charge on the NaNBBS aggregate decreases with the increase in the number of NaNBBS molecules in the aggregate indicating more counter-ion association.     

Tailoring the structure of water at a metal surface: a structural analysis of the water bilayer formed on an alloy template

Recent studies show that structures based on the traditional "icelike" water bilayer are not stable on flat transition metal surfaces and, instead, more complex wetting layers are formed. Here we show that an ordered bilayer can be formed on a SnPt(111) alloy template and determine the structure of the water layer by low energy electron diffraction. Close agreement is found between experiment and the structure calculated by density functional theory. Corrugation of the alloy surface allows only alternate water molecules to chemisorb, stabilizing the H-down water bilayer by reducing the metal-hydrogen repulsion compared to a flat surface.     

Water-filled MCM-41 characterized by double-quantum-filtered2H NMR spectral analysis

The dynamics of water molecules confined in adsorbed layers of siliceous MCM-41 with a pore diameter of 2.8 nm is investigated at 230 K by deuteron nuclear magnetic resonance (NMR) relaxation studies including line shapes of theT ₁ process and double quantum filtered (DQF) spectral analyses.²H DQF NMR is a particularly sensitive tool for the determination of the adsorbate dynamics resulting from residual quadrupolar interaction due to the local order. The amount of monolayer water is determined. The monolayer water is composed of two different water components characterized by water, with isotropic reorientational motions, exchanging with water displaying a solid-like spectrum with 4 kHz edge splitting. One may expect that the latter water is situated on surface sites in MCM-41. The restricted wobbling motion of the D-O bond is used to describe its dynamics which is one order of magnitude slower than the isotropic reorientational motion. The order parameter, the motional correlation time, and the exchange rate thus determined provide useful information on the structure and the adsorptive properties of the mesoporous system.     

Probability distribution function of dipolar field in two-dimensional spin ensemble

We theoretically determine the probability distribution function of the net field of the random planar structure of dipoles which represent polarized particles. At small surface concentrations c of the point dipoles this distribution is expressed in terms of special functions. At the surface concentrations of the dipoles as high as 0.6 the dipolar field obey the Gaussian law. To obtain the distribution function within transitional region c < 0.6, we propose the method based on the cumulant expansion. We calculate the parameters of the distributions for some specific configurations of the dipoles. The distribution functions of the ordered ensembles of the dipoles at the low and moderate surface concentrations have asymmetric shape with respect to distribution medians. The distribution functions allow to calculate various physical parameters of two-dimensional interacting nanoparticle ensembles.     

Surface electromagnetic waves supported by nano conducting layers with inhomogeneities in the conductivity profile

Conducting interfaces and nano conducting layers can support surface electromagnetic waves. Uniform charge layers of non-zero thickness and their asymptotic behavior toward conducting interfaces of infinitely small thicknesses, where the thin charge layer is modeled via a surface conductivity σ _s , are already studied. Here, the possible effects of inhomogeneity in the conductivity profile of the thin conducting layers are investigated for the first time and a new approximate yet accurate enough analytical formulation for mode extraction in such structures is given. In order to rigorously analyze the structure and justify the proposed approximate formulation, the Galerkin’s method with Legendre polynomial basis functions is applied, i.e. the transverse electric field for the TE polarized surface waves and the transverse magnetic field for the TM polarized surface waves are each expanded in terms of Legendre polynomials and then each eigenmode; subjected to appropriate boundary conditions, is sought in the complete space spanned by Legendre basis functions. The proposed approximate solution is then proved to be accurate. In particular, sinusoidal fluctuations are introduced into formerly uniform conductivity profiles and it is numerically demonstrated that surface electromagnetic waves supported by nano conducting layers are not much sensitive to the very shape of conductivity profiles.     

Local electric field and configuration of CO molecules adsorbed on a nanostructured surface with nanocones

Based on the nanostructured surface model that the (platinum, Pt) nanocones grow out symmetrically from a plane substrate, the local electric field near the conical nanoparticle surface is computed and discussed. On the basis of these results, the adsorbed CO molecules are modelled as dipoles, and three kinds of interactions, i.e. interactions between dipoles and local electric field, between dipoles and dipoles, as well as between dipoles and nanostructured substrate, are taken into account. The spatial configuration of CO molecules adsorbed on the nanocone surface is then given by Monte-Carlo simulation. Our results show that the CO molecules adsorbed on the nanocone surface cause local agglomeration under the action of an external electric field, and this agglomeration becomes more compact with decreasing conical angle, which results in a stronger interaction among molecules. These results serve as a basis for explaining abnormal phenomena such as the abnormal infrared effect (AIRE), which was found when CO molecules were adsorbed on the nanostructured transition-metal surface.     

氮掺杂及水分子吸附碳纳米管电子场发射第一性原理研究

对闭口碳纳米管(CNT)顶端分层掺氮及吸附不同数目水分子体系,运用第一性原理研究了有电场存在时的电子场发射性能.结果表明：掺氮并吸附水分子的CNT结构稳定;外电场愈强、水分子数愈多,体系态密度(DOS)向低能端移动幅度愈大且最高分子占据轨道(HOMO)/最低分子空轨道(LUMO)能隙愈小.吸附能,DOS/LDOS,HOMO/LUMO及其能隙分析一致表明,第三层氮掺杂CNT吸附不同数目水分子体系的场发射性能最佳. 关键词： 氮掺杂 水吸附 密度泛函理论 电子场发射