定域片断轨道基组的对称化

片断的UHF运算不能保证每个片断轨道具有确切的电子占据数,故Kost定域化是必需的.当片断产生于多键断裂时,在确保目标轨道单占据性的同时,Kost定域破坏了轨道基组的对称性.为此,在Kost定域化后,必须对单占据轨道作2×2对称化旋转后,再作有条件的RHF运算.以乙烯基片断CHCH(波二烯分子中的一个片断)为例,详述了对称化的方法、原理和计算程序.以C-H片断为例,细述三单键片断轨道基组对称化的特殊性.介绍C-HR参考键长选择的判据,探讨键长与选择Gaussian基组大小的关系.     

最佳定域分子轨道的新算法

本文提出了最佳群对称定域分子轨道（ＯＳＬＭＯＳ）的概念，报道了ＯＳＬＭＯｓ的生成方法。ＯＳＬＭＯｓ满足分子对称、等价与正交；同时最佳逅近经典的非正交价键型轨道，并可作为ＭＣＳＣＦ与ＣＩ方法中的单电子轨道。     

双核锰化合物的定域分子轨道研究

利用ＩＮＤＯ和Ｅｄｍｉｓｔｏｎ－Ｒｕｅｄｅｎｂｅｒｇ定域化方法，计算了Ｍｎ２（μ－Ｃｌ）２（ＣＯ）８和Ｍｎ２（ＣＯ）１０的正则和定域分子轨道，给出了它们的成键图象，讨论了Ｍｎ－Ｍｎ原子间相互作用以及不同方式配位的ＣＯ化学键和几何结构的关系。     

虚轨道定域化

通过引入虚轨道定域化函数，扩展了集居数的定域化方法，在从头算STO－3G水平上用护展后的方法计算无机小分子、烷烃、卤代烷、醇、胺及共轭烃等，结果表明，定域占据轨道与定域虚轨道的系数和能级分布相似的规律。     

定域分子轨道中的σ—π分离

对含重键的分子体系,分子轨道定域化会涉及到两种完全不同的重键描述,即等价的重键或“香蕉”键和不等价的σ和π键,文献曾利用杂化轨道法对此进行过讨论。对于定域分子轨道,具体得出哪种描述取决于所采用的定域准则及计算中采用的近似方法。对于从头算法的定域化研究,Boys定域准则强烈地趋向于等价重键描述;Ruedenberg定域准则只是对未共轭的重键体系有较强的等价重键描述倾向,对共轭的重键体系,这种倾向性明显减     

链烃,环状烃和多面体烃的定域分子轨道研究

采用GAUSSAN 80程序对一系列直链烷烃、环状烃和多面体烷烃进行STO-3G基组下的曲initio计算,在所得非定域分子轨道自洽场结果的基础上,利用Boys方法进行定域化,进而研究了这些分子的定域分子轨道的键弯曲性质、轨道能量和集居数与几何结构之间的关系,用上述结果对一些典型分子的稳定性进行了讨论。     

偶极积分与Boys法分子轨道定域化

定域分子轨道在分子体系的化学图象和物理图象之间充当重要的桥梁作用,它的产生依赖于定域化准则,其中最普遍使用的是Foster-Boys和Edmiston-Ruedenberg(E—R)提出的两种定域化准则。这两种定域化准则是等价的,因而结果也是一致的。但对于E—R定域化来说,由于涉及到大量的多中心积分的计算,计算极为费时,因而远不如Foster-Boys定     

EHMO方法的分子轨道定域化

用Foster-Boys的定域化准则讨论了EHMO方法的分子轨道定域化问题,提出用双中心重叠积分近似计算双中心轨道偶极矩积分方法,得到的EHMO定域分子轨道与严格定域化结果接近,与从头计算方法的定域化结果定性一致。     

轨道定域化中π轨道的自动识别

π轨道的自动识别是片断轨道定的前提。本文介绍并比较了在程序中几种有效的识别方法－ｓ原子轨道系数法,ｐ原子轨道系数法、混合识别法,综合了它们各自的特点和使用范围,使计算机自动识别各类片断分子中的π轨道。     

含三重键有机小分子定域分子轨道的理论研究

为了能够应用定域分子轨道(LMO)模型计算链状有机大分子的光电子能谱,我们已做了一系列工作。本文是用STO-3G基组和Foster-Boys LMO程序,采用文中的计算方法,对含H、C、N和O原子及单,双和叁键的近20个有机小分子进行研究,得到了它们     

Fragment interaction analysis based on local MP2

We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.     

Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus

Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the n-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown, partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables the formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable the determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.     

π和σ体系彻底分离的高度定域的键轨道基组的建立

高度定域的、对称的、键轨道基组的建立是一个多步的计算程序：(1)以定域片断轨道[φk,φi,φj]为基,对分子作有条件的RHF运算,算得FUL和DSI°态的片断分子轨道[Φ°l',Φ°n,Φ°m]和[Φl,Φn,Φm]。在基组[φk,φi,φj]中,φi∈双占据和空σ片断分子轨道(FMOs)组,φj∈πFMO组,φk∈单占据σFMO组,它们都精确地定域在各自的片断内;(2)利用Φ°l'与Φ°l间的重叠积分值(Sl'l>0.5),可以从DSI°态中,自动地选出Ns个对称的、由单占据轨道线性组合而成的分子轨道Φ°l'=Σakl'φk(k=1,2,…,Ns),接着,用Φ°l'取代FUL态中同类的、非对称轨道组Φl=Σaklφk(k=1,2,…,Ns);(3)以上述新的轨道组[Φ°l',Φn,Φm]为基(其中,Φ°l'∈DSI°态,它们离域于整个分子;双占据及空σFMO组Φm和πFMO组Φm属于FUL态),按FUL态的条件,再次对分子作有条件的RHF运算,从中得到一组对称的、闭壳层正则FMOs,而且每一个FMO均有正确的电子占据数;(4)利用Perkin原理,将第3步所得的正则FMO组定域成一个对称的键轨道基组[Φl',Φn',Φm']。在这个基组中,π体系Φm'与σ构架Φn'是彻底分离的,而且这两个轨道组始终精确地定域在各自的片断内。     

识别三唑类农药的片段印迹聚合物的合成及在固相萃取中的应用

采用片段印迹技术, 合成了一系列对7种三唑类农药(三唑酮、烯唑醇、多效唑、烯效唑、戊唑醇、三唑醇和双苯三唑醇)具有识别能力的聚合物. 振荡平衡吸附实验表明, 以邻硝基苯酚为模板的聚合物(M1)对上述7种农药具有最佳的选择性吸附性能. 根据分析物结构对片段印迹聚合物吸附能力的影响, 提出了片段印迹聚合物的识别机理: 三唑类化合物的分子片段末端苯环进入片段印迹聚合物的孔穴中, 同时其羟基与聚合物孔穴外的功能单体4-乙烯基吡啶上的氮原子形成氢键, 二者的协同作用实现对目标分子的选择性识别, 其中分析物末端苯环和聚合物孔穴的匹配是影响片段聚合物识别能力的主要因素. 将基质固相分散(MSPD)与以M1为吸附剂的分子印迹固相萃取(MISPE)联用, 用于土壤样品的前处理. 在3种添加水平下, 各分析物的回收率均为75%~102%, 相对标准偏差为3%~9%(n=5), 方法检出限(信噪比等于3)0.9~15 μg/kg. 表明该分析方法结合了MSPD的快速提取和MISPE的高选择性的特点.     

Theoretical study of energies,structures, and vibrational spectra of the carbonic acid–hydroperoxy radical complexes

In this work, we present the results for the first time of our study on hydrogen‐bonded H₂CO₃–HO₂ complexes (structures 1, 2) by means of ab initio molecular orbital theory. These complexes are important intermediates in the reaction of the hydroperoxy radical and cabonic acid. We calculated that these structures are a six‐membered ring. We found that the binding energy of two complexes are 5.8 and 9.3 kcal/mol using the CCSD(T) method. We also calculated the vibrational and rotational frequencies for these complexes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems

A new computational scheme integrating ab initio multicenter molecular orbitals for determining forces of individual atoms in large cluster systems is presented. This method can be used to treat systems of many molecules, such as solvents by quantum mechanics. The geometry parameters obtained for three models of water clusters by the present method are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article also intended for use in modeling cluster systems using parallel algorithms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1107–1112, 2001     

Investigation of substituent effects in aerogen‐bonding interaction between ZO3 (Z=Kr,Xe) and nitrogen bases

The substituent effects in aerogen bond interactions between ZO₃ (Z = Kr, Xe) and different nitrogen bases are studied at the MP2/aug‐cc‐pVTZ level of theory. The nitrogen bases include the sp bases NCH, NCF, NCCl, NCBr, NCCN, NCOH, NCCH₃ and the sp³ bases NH₃, NH₂F, NH₂Cl, NH₂Br, NH₂CN, NH₂OH, and NH₂CH₃. The nature of aerogen bonds in these complexes is analyzed by means of molecular electrostatic potential, electron localization function, quantum theory atoms in molecules, noncovalent interaction index, and natural bond orbital analyses. The interaction energy (E_int) ranges from ?4.59 to ?9.65 kcal/mol in the O₃Z···NCX complexes and from ?5.30 to ?13.57 kcal/mol in the O₃Z···NH₂X ones. The dominant charge‐transfer interaction in these complexes occurs across the aerogen bond from the nitrogen lone‐pair (n_N) of the Lewis base to the σ*_Z‐O antibonding orbital of the ZO₃. Besides, the formation of aerogen bond tends to decrease the ⁸³Kr or ¹³¹Xe chemical shielding values in these complexes. © 2016 Wiley Periodicals, Inc.     

A core-shell strategy for constructing a single-molecule junction

Understanding the effects of intermolecular interactions on the charge-transport properties of metal/molecule/metal junctions is an important step towards using individual molecules as building blocks for electronic devices. This work reports a systematic electron-transport investigation on a series of "core-shell"-structured oligo(phenylene ethynylene) (Gn-OPE) molecular wires. By using dendrimers of different generations as insulating "shells", the intermolecular π-π interactions between the OPE "cores" can be precisely controlled in single-component monolayers. Three techniques are used to evaluate the electron-transport properties of the Au/Gn-OPE/Au molecular junctions, including crossed-wire junction, scanning tunneling spectroscopy (STS), and scanning tunneling microscope (STM) break-junction techniques. The STM break-junction measurement reveals that the electron-transport pathways are strongly affected by the size of the side groups. When the side groups are small, electron transport could occur through three pathways, including through single-molecule junctions, double-molecule junctions, and molecular bridges between adjacent molecules formed by aromatic π-π coupling. The dendrimer shells effectively prohibit the π-π coupling effect, but at the same time, very large dendrimer side groups may hinder the formation of Au-S bonds. A first-generation dendrimer acts as an optimal shell that only allows electron transport through the single-molecule junction pathway, and forbids the other undesired pathways. It is demonstrated that the dendrimer-based core-shell strategy allows the single-molecule conductance to be probed in a homogenous monolayer without the influence of intermolecular π-π interactions.     

Development of a new density functional program for all-electron calculation of proteins

In this article, we propose a new molecular orbital program for all-electron calculation of proteins which is based on density functional theory. To carry it out in a fully analytical way, we adopted the (pure-) analytical Xα method and modified it for saving a lot of memories for large-scale calculations. The recent software technology sophisticated in information science is inevitably applied to achieve calculations of large molecular systems. The program is coded by the object-oriented language C + +, its output is shown graphically, and the most of the procedures in this program are controlled through an efficient graphical user interface developed by ourselves. Such technology supports the safe construction of the huge software, the tidy representation of enormous data, and the ready control of complex calculations. Test calculations with various sizes of glycine polypeptides indicate that the computation time is proportional to the 1.7 powers of the number of residues. This result suggests that the all-electron calculations of proteins consisting of over 1000 atoms could be performed with distributed and/or massively parallel computers. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 245–256, 1997