A theoretical investigation of Zn?Zn and Be?Be one electron bond

Attachment of one electron to 1,2-diBeX-benzene and 1,2-diZnX-benzene derivatives leads to the formation of stronger Be Be and Zn Zn interaction compared to the neutral one. This is reflected in the dramatic shortening of the Be Be and Zn Zn distance. The formation of these 2-center-1-electron bonds have also been confirmed by topological survey of electron density using quantum theory of atoms in molecules and electron localization function. The formation of these bonds is expected to render stability to these radical anions. These radical anions are stable toward electron detachment and computed bond dissociation energy values are also significant.     

Multidimensional persistence in biomolecular data

Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology. However, its practical and robust construction has been a challenge. We introduce two families of multidimensional persistence, namely pseudomultidimensional persistence and multiscale multidimensional persistence. The former is generated via the repeated applications of persistent homology filtration to high‐dimensional data, such as results from molecular dynamics or partial differential equations. The latter is constructed via isotropic and anisotropic scales that create new simiplicial complexes and associated topological spaces. The utility, robustness, and efficiency of the proposed topological methods are demonstrated via protein folding, protein flexibility analysis, the topological denoising of cryoelectron microscopy data, and the scale dependence of nanoparticles. Topological transition between partial folded and unfolded proteins has been observed in multidimensional persistence. The separation between noise topological signatures and molecular topological fingerprints is achieved by the Laplace–Beltrami flow. The multiscale multidimensional persistent homology reveals relative local features in Betti‐0 invariants and the relatively global characteristics of Betti‐1 and Betti‐2 invariants. © 2015 Wiley Periodicals, Inc.     

原子价壳层电子量子拓扑指数与元素电负性的关系

在基态原子价壳层电子隐核图的基础上, 基于拓扑化学原理以及原子价壳层电子结构特征, 构建了原子价壳层电子量子拓扑指数(AEI), 它对基态原子实现唯一性表征, 结合原子价壳层电子平均化能(∑n_iE_i/∑n_i)等参数, 建立了一套新的元素电负性标度: X_N＝－0.588710AEI₁＋0.761214AEI₂＋0.154982(∑n_iE_i/∑n_i)－0.080929. 该式给出了周期表中氢至镅共95种元素的电负性, 结果表明新电负性标度X_N与Pauling电负性标度颇为一致. 进一步从原子价轨道量子拓扑指数确定了sp, sp², sp³杂化轨道的电负性. 新标度在元素和物质的结构-性质研究中具有一定的适用性.     

SiH_4与Na、Mg和Be等金属氢化物分子间反向氢键相互作用

在B3LYP/6-311++g**、MP2/6-311++g(3df,3pd)及MP2/aug-cc-pvtz水平上分别求得H3SiH…MeHn(Me=Na,Mg,Be;n=1或2)复合物势能面上的3个稳定构型,探讨了以Si-H为电子供体的红移反向氢键相互作用(IHB).经MP2/6-311++g(3df,3pd)水平的计算,在3个复合物中,含基组重叠误差(BSSE)校正的单体间相互作用能分别为-5.98、-8.65和-3.96kJ.mol-1,与MP2/aug-cc-pvtz水平下计算得到的-6.18、-9.12和-4.28kJ·mol-1接近,可见3个反向氢键复合物的相对稳定性顺序为:SiH4...MgH2SiH4...NaHSiH4...BeH2.NBO分析及对相关原子化学位移的计算表明,在复合物中,电子流向总体表现为SiH4→MeHn(n=1或2),且直接参与反向氢键形成的H3的化学位移向低场移动.与传统氢键相比,这里Si1-H3既是氢键供体,又是电子供体,从而形成反向氢键相互作用.另外,采用分子中原子理论(AIM)分别对各复合物中相关键鞍点处的电子密度拓扑性质进行了分析,结果表明3个复合物中均存在以静电性质为主的分子间反向氢键弱相互作用.     

Theoretical study on two types of weak interactions between methylenecyclopropane and XY (X,Y = H,F, Cl,and Br)

We present theoretical evidence that the two types of interactions exist in the complexes formed between methylenecyclopropane (MECP) and XY (X, Y = H, F, Cl, and Br). Two seats of XY interacted with MECP are located: (a) is via the pseudo‐π bonding electron pair associated with a C? C bond of the cyclopropane ring and (b) is via the typical‐π bonding of electron pair of the C?C bond of MECP. These two types of weak interactions are compared based on the calculated geometries, interaction energies, frequency changes, and topological properties of electron density. The integration of electron density over the interatomic surface is found to be a good measure for the strength of weak interaction. Furthermore, the total electron density and separated σ and π electron densities are also computed and discussed in this article. The separated electron density shows σ electron density determined the strength and π electron density influenced the direction of the hydrogen/halogen bond. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Insight into the π‐hole···π‐electrons tetrel bonds between F2ZO (Z = C,Si, Ge) and unsaturated hydrocarbons

The intermolecular π‐hole···π‐electrons interactions between F₂ZO (Z = C, Si, Ge) molecules and unsaturated hydrocarbons including acetylene, ethylene, 1,3‐butadiene and benzene were constructed to reveal the differences of tetrel bonds forming by carbon and heavier tetrel atoms. The ab initio computation in association with topological analysis of electron density, natural bond orbital, and energy decomposition analysis demonstrate that the strength of Si···π and Ge···π tetrel bonds is much stronger than that of C···π tetrel bonds. The Si···π and Ge···π tetrel bonds exhibit covalent or partially covalent interaction nature, while the weak C···π tetrel bonds display the hallmarks of noncovalent interaction, the electrostatic interaction is the primary influencing factor. The Si···π and Ge···π interactions are determined by both the σ‐ and π‐electron densities, while the C···π interactions are dominated mainly by the π‐electron densities. The π‐hole···π‐electrons tetrel bonds are dominated by electrostatic interaction, and polarization has a comparable contribution in the Si···π and Ge···π tetrel bonds.     

Scaling Up DNA Origami Lattice Assembly

The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm² is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm² areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm², this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.     

Structure-activity study of antiepilepticN-aryl-isoxazolecarboxamides/N-isoxazolylbenzamide analogs using Wiener's topological index

The relationship between Wiener's topological index and the antiepileptic activity of a series ofN-aryl-isoxazole carboxamides/N-isoxazolylbenzamide analogs has been investigated. Values of Wiener's topological index for 69 compounds constituting the training set were computed and an active range was identified. Each analog was subsequently assigned an activity which was then compared with the reported antiepileptic activity against the maximal electroshock seizure (MES) test. Due to significant correlation between antiepileptic activity and Wiener's topological index, it was possible to predict antiepileptic activity with an accuracy of 91 % in the active range.     

人工神经网络法预测炸药组分的色谱保留值参数

 以分子拓扑指数作为炸药组分的结构描述符 ,利用反向传播算法 (BP)人工神经网络 ,以Sigmoid函数为传递函数 ,分子连接性指数0 χ ,1χ ,2 χ与边邻接指数 (ε)为输入向量 ,反相高效液相色谱保留值参数logkw 和S为输出向量 ,将输入向量归一化至 - 3～ 3区间 ,输出向量归一化至 0～ 1区间 ,网络精度取 0 5 ,学习步长 η的初始值取0 2 ,动量因子α取 0 5 ,通过对 2 0种炸药的网络模型进行训练 ,建立了炸药分子结构与logkw 和S之间的定量模型。结果表明 ,该模型较好地反映了炸药分子结构与保留值之间的关系。