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。团簇埋入自洽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。本文介绍了上述计算的基本理论、方法和结果。     

4,4’-对苯巯基醚分子器件的几何结构及其电学性质的研究（英文）

从第一性原理出发,用弹性散射格林函数的方法计算了4,4-对苯巯基醚分子器件几何结构的变化对其电子结构及其电学性质的影响.计算结果表明,选择不同的电极间距会引起电子输运峰的高度和分子与电极的耦合程度的变化,同时也对分子电流和电导的开启位置有较小的影响,进而使分子体系的电输运性质表现各异     

B3分子的结构和热能函数

利用从头计算法QCISD／6－311G确定了B3分子的基电子态,并计算了结构参数。采用原子分子反应静力学原理推导了其离解极限。在此基础上,用多体展式法导出了B3（X^2A’1）的解析势能函数,可用于进一步的计算研究。通过势能函数等值图和三维图分析和展求了B3分子的结构特点,并指出由B2到B3分子的最可能途径。     

利用电子结构数据拟合H2分子的电子壳模型势函数参数

电子壳模型势函数在离子晶体的原子级计算机模拟中有广泛应用,其势参数主要通过拟合晶体的实验数据或电子结构数据得到.提出了通过拟合双原子分子的量子化学从头计算电子结构数据来获得该势函数的方法,并由H2分子的电子结构数据建立了H原子间的电子壳模型势函数.此外,还应用该势函数对H+2分子离子进行了计算.该势函数拟合方案更适合于共价键型的分子.     

官能团对分子器件电输运特性的影响

以4,4′-二巯基联苯分子为研究对象,利用第一性原理计算方法和非平衡格林函数理论,研究了官能团氨基和硝基对分子的电子结构以及分子结电输运性质的影响. 计算结果表明,在分子的不同位置添加同一类官能团氨基会使分子的电子结构发生变化,从而影响分子结的电输运性质. 而在分子的同一位置添加不同类型的官能团氨基和硝基则对分子间的相互作用有着显著影响,会使分子发生转动,从而改变分子的几何结构和电子结构,影响分子结的电输运特性. 并且发现随着分子的转动,添加官能团硝基时分子会呈现出记忆功能. 关键词： 官能团 电子输运 分子电子学     

有机分子电子输运性质的计算与分析

从第一性原理出发,采用杂化的密度泛函理论和弹性散射格林函数法,计算有机分子4,4'-二巯基二苯醚分子的电子结构并研究其电子输运性质.计算结果表明,电场对分子系统电子结构有明显的影响,电流、电导表现为非线性变化,与不考虑电场作用时相比,更为接近实验结果.     

分子和金表面相互作用的DFT和HF研究之比较

从第一性原理出发,分别利用密度泛函理论和哈特利-福克方法优化了4 ,4-二巯基联苯分子的几何结构,计算了电子结构,讨论了分子与金表面的相互作用.结果表明,在描述分子的电子结构以及分子与金表面的相互作用时,密度泛函理论可以给出更好的结果.     

（CdS）n分子簇电子结构性质的赝势从头算研究

本文运用赝势从头计算法对（ＣｄＳ）ｎ分子簇电子结构进行了精确的量子化学计算研究，计算结果表明：随着ＣｄＳ个数的增加，ＣｄＳ单元之间的相互作用增强，ＣｄＳ之间共价键成份减少，离子键成份增加。     

分子的位置取向对分子器件电输运特性的影响

以1,4-二硫酚(DTB)分子为研究对象，利用第一性原理计算方法和非平衡格林函数理论，研究了分子的位置取向对分子电子结构以及分子结电输运性质的影响.计算结果表明，分子位置取向的改变会影响分子的电子结构，从而影响分子体系的电输运特性，扩展分子的平衡态不是电子输运的最佳状态，适当调节分子的位置取向可以提高分子的电输运特性. 关键词： 位置取向 电子输运 分子电子学     

(Zn,Al)O电子结构第一性原理计算及电导率的分析

采用第一性原理平面波赝势方法和广义梯度近似计算了ZnO与(Zn,Al)O的电子结构.结合分子轨道理论,从原子布居、键布居、能带结构和态密度角度分析了掺Al前后ZnO的成键情况及对电子间相互作用的影响.利用第一性原理计算结果理论推导计算了(Zn,Al)O的载流子浓度并进一步分析了ZnO电导率的变化情况.与实验结果比较可知,掺Al后ZnO载流子浓度增加,并且ZnO的电导率比未掺杂时有了显著的提高. 关键词： 第一性原理 电子结构 电导率 (Zn Al)O     

Refining Fermi surface topologies from ab initio calculations through momentum density spectroscopies

It is well known that the agreement between the Fermi surface topologies predicted by ab initio electronic structure calculations and experiment can often be brought into much better agreement through small rigid-band-like shifts. A new method for refining these calculations using experimental data containing Fermi surface information, based on a rigid-band-like fitting approach is presented. In this method, experimental data from different methods can be combined to refine and deliver a ‘tuned’ bandstructure, allowing an investigation of FS nesting properties, a quantitative comparison between experiment and calculation, and highlighting the origin of inconsistencies. Results of the application of this method to positron annihilation experiments in vanadium are presented, showing significant improvement over the ab initio calculation. In order to demonstrate the versatility of this fitting method, it has been applied to a combination of positron annihilation measurements and magnetic Compton scattering experiments in ferromagnetic nickel.     

LSDA+U方法对富勒烯内掺稀土原子的结构和电子结构的理论研究

在密度泛函理论框架下的局域密度近似方法 (LDA)能够准确地给出广延态电子体系的基态电子结构 ,是研究复杂体系的电子结构的一种非常成功的方法。由于这种方法不含参数 ,被广泛地用于微观体系的研究。但是 ,在处理的体系中含有局域电子时 ,由于方法的局限 ,给出的结果与光电子谱等试验结果符合得并不好。LSDA U方法是在局域自旋密度近似的框架下 ,结合模型哈密顿方法 ,对局域电子采用哈伯德模型描述 ,用以改进局域密度近似计算的一种方法。本文利用局域密度近似下的离散变分团簇方法 (DVM )对于内嵌稀土原子的富勒烯Er2 @C82 、Tm @C82 的电子结构进行了第一性原理的计算。对于体系中所含的稀土原子存在强关联的 4f电子 ,在LDA方法计算的基础上 ,考虑 4f电子在位库仑作用 ,用LSDA U方法研究了上述体系 ,得到了可以和XPS和吸收谱相比较的结果。     

NiAl的几何与电子结构

关键词：     

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.     

Nb原子链的结构稳定性和电子性质

使用基于密度泛函理论的第一性原理平面波赝势法，研究了Nb原子链的结构稳定性和电子结构性质.计算表明，Nb原子可以形成线性链，平面之字形，二聚化以及梯子形等一系列的一 维链式结构.结果也显示，其中之字形结构最为稳定，其他结构均为亚稳的.通过第一性原理 计算的电子结构和Jahn-Teller效应，讨论了这些结构的相对稳定性以及各链式结构的电子 能带、态密度和电荷密度等性质. 关键词： Nb原子链 结构稳定性 电子结构 从头计算     

Comparative Ab initio analysis of valence XPS data for acenes and paraphenyl oligomers: Application of the molecular-orbital intensity model

The electronic structures of acenes and paraphenyls are approached by ab initio calculations and XPS valence data. Particular attention is drawn to the molecular-orbital intensity model, which proves to be a quite successful means of following the evolution of all the valence orbitals as a function of system size.     

Three-dimensional Wentzel–Kramers–Brillouin approach for the simulation of scanning tunneling microscopy and spectroscopy

We review the recently developed three-dimensional (3D) atom-superposition approach for simulating scanning tunneling microscopy (STM) and spectroscopy (STS) based on ab initio electronic structure data. In the method, contributions from individual electron tunneling transitions between the tip apex atom and each of the sample surface atoms are summed up assuming the one-dimensional (1D) Wentzel–Kramers–Brillouin (WKB) approximation in all these transitions. This 3D WKB tunneling model is extremely suitable to simulate spin-polarized STM and STS on surfaces exhibiting a complex noncollinear magnetic structure, i.e., without a global spin quantization axis, at very low computational cost. The tip electronic structure from first principles can also be incorporated into the model, that is often assumed to be constant in energy in the vast majority of the related literature, which could lead to a misinterpretation of experimental findings. Using this approach, we highlight some of the electron tunneling features on a prototype frustrated hexagonal antiferromagnetic Cr monolayer on Ag(111) surface. We obtain useful theoretical insights into the simulated quantities that is expected to help the correct evaluation of experimental results. By extending the method to incorporate a simple orbital dependent electron tunneling transmission, we reinvestigate the bias voltage- and tip-dependent contrast inversion effect on theW(110) surface. STM images calculated using this orbital dependent model agree reasonably well with Tersoff-Hamann and Bardeen results. The computational efficiency of the model is remarkable as the k-point samplings of the surface and tip Brillouin zones do not affect the computational time, in contrast to the Bardeen method. In a certain case we obtain a relative computational time gain of 8500 compared to the Bardeen calculation, without the loss of quality. We discuss the advantages and limitations of the 3D WKB method, and show further ways to improve and extend it.     

Charge distributions in metallic alloys: a charge-excess functional theory approach

The distribution of local charge (DLC) excesses in metallic alloys, previously obtained as a result of the analysis of order N electronic structure calculations, is derived from a variational principle. A phenomenological charge-excess functional theory is obtained which is determined by three concentration dependent, material specific parameters that can be obtained from ab initio calculations. The theory requires modest computational efforts and reproduces with an excellent accuracy the DLC and the electrostatic energies of ordered, substitutionally disordered, or segregating metallic alloys and, hence, can be considered an efficient approach alternative to conventional electronic structure calculations. The substantial reduction of computing time opens new perspectives for the understanding of metallic systems and their mechanical properties.