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 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.     

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.     

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     

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.     

Simulation of electronic structure Hamiltonians using quantum computers

Over the last century, a large number of physical and mathematical developments paired with rapidly advancing technology have allowed the field of quantum chemistry to advance dramatically. However, the lack of computationally efficient methods for the exact simulation of quantum systems on classical computers presents a limitation of current computational approaches. We report, in detail, how a set of pre-computed molecular integrals can be used to explicitly create a quantum circuit, i.e. a sequence of elementary quantum operations, that, when run on a quantum computer, obtains the energy of a molecular system with fixed nuclear geometry using the quantum phase estimation algorithm. We extend several known results related to this idea and discuss the adiabatic state preparation procedure for preparing the input states used in the algorithm. With current and near future quantum devices in mind, we provide a complete example using the hydrogen molecule of how a chemical Hamiltonian can be simulated using a quantum computer.     

Density-functional theory study on the electronic properties of laves phase superconductor CaIr_2

In this work we have used density-functional theory methods such as full-potential local orbital minimum basis(FPLO) and ELK-flapw to study the electronic structure of newly discovered Laves phase superconductor CaIr_2.The calculation of density of states(DOS) indicates that the bands near Fermi level are mostly occupied by the d-electrons of iridium.The simulation of de Haas-van Alphen(dHvA) effect has been performed by using Elk code to check the Fermi surface topology.The results show that there exist four Fermi surfaces in CaIr_2,including two electron-type and two hole-type surfaces.The optical response properties of CaIr_2 have been calculated in the dipole-transition approximations combined with including intra-band Drude-like terms.In the optical spectrum σ(ω) shows that the crossover from intraband to inter-band absorption occur near 1.45 eV.Further analysis on the electron energy loss spectra(EELS) matches the conclusion from that of optical conductivity σ(ω).     

几种三元过渡金属碳化物弹性及电子结构的第一性原理研究

基于密度泛函理论平面波方法研究了六方WC型Re_xW_1－xC(x=1, 0.25, 0.75, 0),Re_0.5Os_0.5C和Os_0.5W_0.5C的晶体结构、弹性和电子结构性质.研究发现Re_0.25W_0.75C晶体具有优异的弹性性能及稳定性,其剪切模量(312 GPa)超过了所有其他实验合成和     

First-principle study of the structural,electronic,and optical properties of SiC nanowires

We preform first-principle calculations for the geometric, electronic structures and optical properties of SiC nanowires(NWs). The dielectric functions dominated by electronic interband transitions are investigated in terms of the calculated optical response functions. The calculated results reveal that the SiC NW is an indirect band-gap semiconductor material except at a minimum SiC NW(n = 12) diameter, showing that the NW(n = 12) is metallic. Charge density indicates that the Si–C bond of SiC NW has mixed ionic and covalent characteristics: the covalent character is stronger than the ionic character, and shows strong s–p hybrid orbit characteristics. Moreover, the band gap increases as the SiC NW diameter increases. This shows a significant quantum size and surface effect. The optical properties indicate that the obvious dielectric absorption peaks shift towards the high energy, and that there is a blue shift phenomenon in the ultraviolet region. These results show that SiC NW is a promising optoelectronic material for the potential applications in ultraviolet photoelectron devices.     

Optimized geometry and electronic structure of graphyne-like silicyne nanoribbons

Silicyne, a silicon allotrope, which is closely related to silicene and has graphyne-like structure, is theoretically investigated in this work. Its optimized geometry and electronic band structure are calculated by means of the first-principles frozen-core projector-augmented wave method implemented in the Vienna ab initio simulation package (VASP). We find that the lattice parameter is 9.5, the silicon chain between hexagons is composed of disilynic linkages (-Si≡Si-) rather than cumulative linkages (=Si=Si=), and the binding energy is 3.41 eV per atom. The band structure is calculated by adopting the generalized gradient approximation and hybrid functionals. The band gap produced by the HSE06 functional is 0.73 eV, which is nearly triple that by the generalized gradient approximation of Perdew-Burke-Ernzerhof functional.     

T型石墨烯及其衍生物的结构与电子特性

采用基于密度泛函理论的第一原理方法研究了T型石墨烯及其衍生物-n(n=1—5)的结构稳定性和电子结构性质.T型石墨烯是一种拥有四角形环的二维碳材料同素异构体,通过改变连接四角形环的碳链上的碳原子个数n,可以得到一系列的sp-sp~2杂化结构,称其为T型石墨烯衍生物-n.计算结果表明:这些材料的结构稳定性、化学键类型和电子结构性质都依存于n的奇偶性.其中T型石墨烯(n=0)的结构最稳定,并形成一个由8个碳原子构成的大环.声子谱计算的结果表明,n为偶数时的体系具有动力学稳定性,而n为奇数时的体系则是不稳定的.n为偶数时体系四角形环之间的碳链上的化学键呈单、三键交叉排列,体系显示为金属性特征,且随着n的增大,体系的金属性加强.n为奇数时体系四角形环之间的碳链上的化学键则为双键连续排列,体系呈金属性且具有磁性(n=1除外).研究表明该系列材料作为一种新的二维碳材料同素异构体,具有独特的结构和丰富的电子结构特性,很可能在纳米器件中得到广泛应用.     

Ti掺杂NbSe2电子结构的第一性原理研究

采用基于密度泛函理论框架下的第一性原理平面波超软赝势方法, 计算了理想2H-NbSe₂和Ti掺杂2H-NbSe₂晶体的几何结构及电子结构; 对掺杂前后超胞的能带图、态密度及分波态密度图进行了分析. 结果表明, 掺杂后费米能级附近能量区域的电子态密度出现了较高的峰值, 且费米能级位置发生了改变. 理论上可以认为Ti的掺杂会使得NbSe₂的导电性增强, 有利于开发新型的电接触复合材料.     

Cluster calculation of electronic structure and hyperfine interactions for α-Fe2O3

The MSX_α cluster technique has been used to study the electronic structure of hematite α-Fe₂O₃, where iron is formally in a 3d₅⁶S state. The calculated energy levels are compared with X-ray emission and photoelectron spectra. The wave functions have been used to compute the charge distribution, as well as hyperfine parameters such as quadrupole coupling constant, isomer shift and magnetic hyperfine field. The results indicate a considerable influence of chemical bonding on these parameters due to charge transfer and covalency. From the calculated field gradient and the measured quadrupole coupling constant a nuclear quadrupole moment for ^57mTe of about 0.11b is deduced. This value is smaller than the most recent estimates of 0.15b based on the ionic model but not as small as the value of 0.082b obtained from first principles calculations on iron dihalides.     

固态二氧化碳电子结构及性能的理论研究

采用基于赝势平面波理论的第一性原理计算方法,研究了9种结构的固态二氧化碳的结构和性质.经过结构的几何优化,得到α石英稳定结构晶格常数与他人的计算值基本一致.通过对平衡态能量的分析,我们得出β方石英(cristobalite)结构是能量最低的结构.这与文献的研究结果一致.对弹性性质的计算结果表明,除了超石英(stishovite)和立方黄铁矿(cubic-pyrite)结构之外,其他的结构都是弹性稳定的.利用基于Mulliken轨道重叠布居数的共价固体本征硬度计算方法,预测了各个结构的本征硬度值.结果表明, 关键词： 第一性原理计算 固态二氧化碳 电子结构 硬度     

表面氢化双层硅烯的结构和电子性质

采用密度泛函理论(DFT)广义梯度近似GGA和HSB06方法研究了氢化双层硅烯(silicene)的结构和电子性质, 结果表明: 氢化后的双层硅烯可能存在三种稳定的构型, AA椅型、AB椅型和AA船型, 其中AA椅型和AB椅型结构最为稳定, 氢化后这三种稳定构型材料的性质由零带隙的半金属(semimetal)转变为禁带宽度分别为1.208, 1.437和1.111 eV 的间接带隙的半导体, 采用混合泛函HSB06计算修正得到的带隙分别为1.595, 1.785 和1.592 eV. 进一步分析了在双轴应变下氢化双层硅烯的带隙随应变的关系, 得到应变可以连续的调节材料的带隙宽度, 这些性质有可能应用于未来的纳米电子器件.     

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。     

High-throughput identification of one-dimensional atomic wires and first principles calculations of their electronic states

Low dimensional materials are suitable candidates applying in next-generation high-performance electronic, optoelectronic, and energy storage devices because of their uniquely physical and chemical properties. In particular, onedimensional(1 D) atomic wires(AWs) exfoliating from 1 D van der Waals(vd W) bulks are more promising in next generation nanometer(nm) even sub-nm device applications owing to their width of few-atoms scale and free dandling bonds states. Although several 1 D AWs have been experimentally prepared, few 1 D AW candidates could be practically applied in devices owing to lack of enough suitable 1 D AWs. Herein, 367 kinds of 1 D AWs have been screened and the corresponding computational database including structures, electronic structures, magnetic states, and stabilities of these 1 D AWs has been organized and established. Among these systems, unary and binary 1 D AWs with relatively small exfoliation energy are thermodynamically stable and theoretically feasible to be exfoliated. More significantly, rich quantum states emerge,such as 1 D semiconductors, 1 D metals, 1 D semimetals, and 1 D magnetism. This database will offer an ideal platform to further explore exotic quantum states and exploit practical device applications using 1 D materials. The database are openly available at http://www.dx.doi.org/10.11922/sciencedb.j00113.00004.     

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     

Simulation of electronic structure of nanomaterials by central insertion scheme

An effective central insertion scheme (CIS) that allows to study the electronic structure of nanomaterials at the first principles level is introduced. Taking advantage of advanced numerical methods, such as the implicitly restarted Arnoldi method (IRAM) and spectral transformation, together with efficient parallelization technique, this scheme can provide accurate electronic structures and properties of one-, two-, and three-dimensional nanomaterials with only a fraction of computational time required for conventional quantum chemical calculations. Electronic structures of several nanostructures, such as single-walled carbon nanotubes of sub-100 nm in length, silicon nanoclusters of sub-6.5 nm in diameter and metal doped silicon clusters, calculated at hybrid density functional level are presented.      

ZnO原子链的结构稳定性和电子性质的第一性原理研究

本文采用基于密度泛函理论的第一性原理平面波赝势法,研究了ZnO原子链的结构稳定性和电子性质.结果表明：ZnO分子可以形成直线形结构、梯子形结构以及双梯子形结构等一维链式结构,而之字形链状结构是不能稳定存在的.计算结果也表明：这些稳定存在的一维原子链结构均表现出间接带隙的特征,而之字形结构的原子链却表现出了类似金属的能带特征. 关键词： 原子链 结构稳定性 电子结构 第一性原理计算