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.     

Molecular properties and potential energy function model of BH under external electric field

Using the density functional B3P86/cc-PV5Z method, the geometric structure of BH molecule under different external electric fields is optimized, and the bond lengths, dipole moments, vibration frequencies, and other physical properties parameters are obtained. On the basis of setting appropriate parameters, scanning single point energies are obtained by the same method and the potential energy curves under different external fields are also obtained. These results show that the physical property parameters and potential energy curves may change with external electric field, especially in the case of reverse direction electric field. The potential energy function without external electric field is fitted by Morse potential, and the fitting parameters are obtained which are in good agreement with experimental values. In order to obtain the critical dissociation electric parameter, the dipole approximation is adopted to construct a potential model fitting the corresponding potential energy curve of the external electric field. It is found that the fitted critical dissociation electric parameter is consistent with numerical calculation, so that the constructed model is reliable and accurate. These results will provide important theoretical and experimental reference for further studying the molecular spectrum, dynamics, and molecular cooling with Stark effect.     

The response of temperature and hydrostatic pressure of zinc-blende GaxIn1-xAs semiconducting alloys

<正>The electronic band structure of Ga_xIn_1-xAs alloy is calculated by using the local empirical pseudo-potential method including the effective disorder potential in the virtual crystal approximation.The compositional effect of the electronic energy band structure of this alloy is studied with composition x ranging from 0 to 1.Various physical quantities such as band gaps,bowing parameters,refractive indices,and high frequency dielectric constants of the considered alloys with different Ga concentrations are calculated.The effects of both temperature and hydrostatic pressure on the calculated quantities are studied.The obtained results are found to be in good agreement with the available experimental and published data.     

Solution of Dirac equation around a charged rotating black hole

The aim of this paper is to solve the radial parts of a Dirac equation in Kerr-Newman （KN） geometry. The potential is replaced by a collection of step functions, then the reflection and transmission coefficients as well as the solution of the wave equation are obtained by using a quantum mechanical method. The result shows that the waves with different values of mass will be scatted off very differently.     

Absolute Differential Cross Sections for Elastic Scattering of Electrons from CO at Intermediate and High Energies

The additivity rule model together with the complex optical model potential correlated by the concept of bonded atoms, which considers the overlapping effect of electron clouds between two atoms in a molecule, is firstly employed to calculate the absolute differential cross sections for electrons scattered by carbon monoxide at intermediate and high energies at the Hartree-Fock level. A comparison of elastic differential cross section results, obtained by using the correlated complex optical model potential, with the available experimental data,shows a significant improvement over the uncorrelated ones. The differential cross sections obtained by using thecorrelated complex optical model potential are in very good agreement with the experimental data. It is shown that the additivity rule model together with the correlated complex optical model potential is suitable for the calculations of the absolute differential cross sections of e-CO scattering.     

Depletion interactions in binary mixtures of repulsive colloids

Acceptance ratio method, which has been used to calculate the depletion potential in binary hard-sphere mixtures, is extended to the computation of the depletion potential of non-rigid particle systems. The repulsive part of the Lennard-Jones pair potential is used as the direct pair potential between the non-rigid particles. The depletion potential between two big spheres immersed in a suspension of small spheres is determined with the acceptance ratio method through the application of Monte Carlo simulation. In order to check the validity of this method, our results are compared with those obtained by the Asakura-Oosawa approximation, and by Varial expansion approach, and by molecular dynamics simulation. The total effective potential and the depth of its potential well are computed for various softness parameters of the direct pair potential.     

Application of Complete Orthonormal Sets of Ψα-Exponential-Type Orbitals to Accurate Ground and Excited States Calculations of One-Electron Diatomic Molecules Using Single-Zeta Approximation

The applicability of the complete orthonormal sets of ψ^a-exponential-type orbitals introduced by one of the authors to the study of electronic structure of one electron diatomic molecules is demonstrated using single-zeta approximation. As an example of application, tile calculations have been performed for o, 7r and 5 states of one electron homo- and hetero-nucleac diatomic molecules H＋2 and Hell2＋, respectively. The calculation results are presented. The values for these molecules obtained in eight-digit accuracy ace close to the results of solution presented in literature.     

Surface Effects on Wannier Excitons in Superlattices:Monte Carlo Simulation

Using a Monte Carlo quadrature,we calculate by a variational method the binding energy Eb of Wannier excitons in N-period m-CdMnTe/n-CdTe superlattices,including or not including the step discontinuity in the potential barrier at the interface,and with varying N as well as well width.The calculation is performed in the framework of the effective mass approximation for both heavy-hole and light-hole excitons.The degree of exciton localization dependence on these parameters is accurately illustrated.     

Anomalously Strong Scattering of Spontaneously Produced Laser Radiation in the First Free-Electron Laser and Study of Free-Electron Two-Quantum Stark Lasing in an Electric Wiggler with Quantum-Wiggler Electrodynamics

We calculate the scattering cross section of an electron with respect to the spontaneously produced laser radiation in the first free-electron laser （FEL） with quantum-wiggler electrodynamics （QWD）. The cross section is 1016 times the Thomson cross section, confirming the result obtained by a previous analysis of the experimental data. A QWD calculation show that spontaneous emission in an FEL using only an electric wiggler can be very strong while amplification through net stimulated emission is practically negligible.     

DFT study on the structure and spectra of GasP5 cluster

In this paper, possible structures of GasP5 cluster were optimized by using density functional method with generalized gradient correction （B3LYP）. The electronic structure of the isomers with lower energy was studied. The most stable structure obtained for GasP5 is a distorted pentaprism. The Ga-P bond formed in the cluster is strongly ionic. Based on NBO analysis, an average value of 0.59 electron transfers from Gallium to Phosphorus. The bond length 2.33-2.43 is around the value in bulk GaP. The HOMO-LUMO gap is about 2.2 eV. The dipole moment and polarizability are calculated, and the IR and Raman spectra are also presented.     

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.     

Transition moments and NH2 cometary spectra

We calculate vibronic transition moments for the A^?2A_1-X^?2, electronic band system, and for the vibrational transitions within the à and [Xtilde] states, of the NH₂ free radical with the purpose of assisting in the quantitative interpretation of cometary NH₂ emission spectra. To do this it is necessary to use molecular wavefunctions, and electric dipole moment and transition moment surfaces. The wavefunctions are obtained using our program system RENNER after we have determined optimized à and [Xtilde] state potential energy surfaces in a fitting to data. We have obtained the electric dipole moment and transition moment surfaces by ab initio calculation.     

A study of the vibrations of fluoroform with a sixth order nine-dimensional potential: a combined perturbative-variational approach

A full dimensional calculation of the vibrational eigenstates and spectrum of CHF₃, using Van Vleck perturbation theory followed by a variational calculation, is presented. For this, a Taylor series expansion of the potential which includes important terms up to sixth order is obtained. The importance of the quintic and sextic terms is established by comparison of states obtained with and without these terms. Adjusting the potential slightly for better agreement with experiments, we have computed all the eigenstates below 6500cm^?1. These states are used with an ab initio dipole moment surface to calculate transition intensities from the ground state. The calculated results agree well with experimental findings.     

Effect of the degree of ordering of structural vacancies on the fine structure of the valence-band top in cubic boron nitride

The electronic energy structure of the defect system of c-BN_x with ZnS-type structure is calculated in the multiple-scattering theory by the local coherent potential method. The cluster version of the MT approximation is used to calculate the crystal potential. The effect of the relaxation of the crystal lattice on the electronic structure of nonstoichiometric boron nitride c-BN_0.75 is studied and a comparison is made with the electronic energy structure of c-BN in the same approximation. Fiz. Tverd. Tela (St. Petersburg) 39, 1064–1065 (June 1997)     

GaN及其Ga空位的电子结构

用团簇埋入自洽计算法对宽禁带半导体GaN的电子结构进行了自旋极化的、全电子、全势场的从头计算,得到了与实验值符合的GaN晶体禁带宽度以及价带中N2p带、N2s带和Ga3d带之间的相对位置.在此基础上Ga空位计算(无晶格畸变)显示,Ga空位周围的费米面显著高于正常GaN晶格的费米面.因此Ga空位周围N原子的处于费米面上的2p电子很易被激发成正常晶格处的传导电子 关键词： GaN 电子结构 团簇埋入自洽计算     

蛋白质分子电子结构的第一性原理从头计算

蛋白质分子电子结构的计算对生命科学和计算机药物设计有重要的科学意义和应用价值,但对计算方法和计算机也是巨大的挑战。团簇埋入自治计算法是近年来发展起来的“第一性原理”、从头计算法。它采用局域化无相互作用单电子模型,结合“分块－合拢”技术,使计算量大大减少。最近,应用该方法,对一个真实蛋白质分子（南瓜种子中的胰蛋白酶抑止因子ＣＭＴＩ－Ｉ）电子结构的首次“第一性原理”、全电子、全势场、从头计算获得成功。表明生物大分子电子结构的计算在现有计算机条件下已成为现实,使从本质上揭开生命奥秘成为可能。本介绍了上述计算的基本理论、方法和结果。     

LaNi5晶体表面态的计算研究

用“团簇埋入自洽计算法”对LaNi₅晶体表面进行了全电子、全势场、自旋极化的从头计算. 在原子纵向坐标充分弛豫的条件下，得到处于最低基态总能量下LaNi₅晶体的非平整表面空间结构及其电子结构. LaNi₅晶体最表面La原子向外凸出，Ni原子向里收缩，凹凸不平的表面层增加了表面原子与氢原子的接触面积；而表面层的有效体积增大了约9%，有利于氢原子的进入. LaNi₅晶体表面态的费米能量大大高于体材料的费米能量. 在费密面上主要是Ni的3d电子，价带未填满，显示金属性. LaNi₅晶体表面第一、第二层有1.15个电子从La原子向Ni原子转移，这两层有反向的微小自旋磁矩，从而使表面显示顺磁性. 得到了LaNi₅晶体表面的价带电子态密度. 用过渡态方法计算了LaNi₅晶体表面的电离能和电子亲和势. 所有计算结果显示：LaNi₅晶体表面的性质与体性质显著不同，而与氢化物LaNi₅H₇的性质非常相近. 这说明LaNi₅晶体的表面结构有利于氢原子的吸收. 关键词： 5')" href="#">LaNi₅ 表面 电子结构 团簇埋入自洽计算法