Unique description of chemical structures based on hierarchically ordered extended connectivities (HOC procedures). I. Algorithms for finding graph orbits and canonical numbering of atoms

An iterative algorithm is described for finding topological equivalence, ordering, and canonical numbering of vertexes (atoms) in molecular graphs. Like the Morgan algorithm, it is based on extended connectivities but: (i) the latter are used hierarchically, i. e., the discrimination in the next iteration is carried out only for the vertices having the same extended connectivities (ranks) at the previous iteration; (ii) at equal extended connectivities, additional discrimination is introduced by the ranks of adjacent vertices; (iii) there is no “best name” search; (iv) three levels of complexity of chemical structures are distinguished and handled by different procedures. Two schemes of application of HOC procedures are presented: one directed towards a fast canonical numbering for coding systems, and another one yielding levels of topological equivalence allowing a unique topological representation of the molecule with possible applications to similarity search, structure-activity correlations, etc.     

Computer enumeration of polyhexes using the compact naming approach

The enumeration of polyhexes can be easily carried out by utilizing a compact name (CN) approach to code chemical structures. The Fortran program performing generation of benzenoid hydrocarbons with 1–10 rings is presented. The computed structures are divided into various classes according to their cata- or peri- as well and non- or radicaloid character. Use of the additive nodal increments (ANI) approach leads to algorithm producing representative samples of the polyhexes' sets which can be applicable in testing of various topological formulae.     

Paneth,IUPAC, and the Naming of Elements

The procedure for assigning names to elements by the International Union of Pure and Applied Chemistry involves establishing priority of discovery, then inviting the discoverers to suggest a name. This protocol is in contrast with the suggestions of Friedrich A. Paneth form 1947, who believed that the discoverers of an element have the undisputed right to name it. This difference in philosophy came to light during a workshop convened 10 years ago for the purpose of naming elements 104–109, when the discoverers of these elements contended that they were solely entitled to name them. During the debate, and in support of the name seaborgium for element 106, it was argued that gadolinium, samarium, gallium, einsteinium and fermium had been named after living scientists. The history of the naming of these elements demonstrates that this is not the case; Glenn T. Seaborg is the first scientist for whom an element was named during his lifetime.     

Unique description of chemical structures based on hierarchically ordered extended connectivities (HOC procedures). III. Topological,chemical, and stereochemical coding of molecular structure

A topological code is devised on the basis of the unique topological representation of the molecule described in the preceding two parts of this series.¹ By adding to the topological code additional chemical information on atoms and/or bonds, as well as stereochemical information, a chemical and respectively stereochemical code (SHOC) are also constructed. The advantages of the new linear codes are that they are convention-free codes, preserving the symmetry of molecular graph, and easily implemented either manually or by means of computer programs. By concentrating all topological, chemical, and stereochemical information, our code (SHOC) is more compact and more general than the codes based on several separate lists.     

Chemical signed graph theory

Chemical signed graph theory is presented. Each topological orbital of an N-vertex molecular graph is represented by a vertex-signed graph (VSG ) that is generated by assigning a sign, either plus or minus, to the vertices without solving the secular matrix equation. The bonding capacity of each VSG is represented by its corresponding edge-signed graph (ESG ) and is quantified by the net sign of the ESG . The resulting 2^N–1 configurations of VSG s can be divided into several groups according to the net signs of the corresponding ESG s. Summation of an appropriate set of degenerate VSG s is found to yield the conventional, canonical molecular orbitals. The distribution of the number of VSG s with respect to the net sign is found to be binomial, which can be related to bond percolation in statistical physics. © 1994 John Wiley & Sons, Inc.     

拓扑绝缘体二维纳米结构与器件

拓扑绝缘体是一种全新的量子功能材料, 具有绝缘性体能带结构和受时间反演对称性保护的自旋分辨的金属表面态, 属于Dirac 粒子系统, 将在新原理纳电子器件、自旋器件、量子计算、表面催化和清洁能源等方面有广泛的应用前景. 理论和实验相继证实Sb₂Te₃, Bi₂Se₃和Bi₂Te₃单晶具有较大的体能隙和单一Dirac 锥表面态, 已经迅速成为了拓扑绝缘体研究中的热点材料. 然而, 利用传统的高温烧结法所制成的拓扑绝缘体单晶块体样品常存在大量本征缺陷并被严重掺杂, 拓扑表面态的新奇性质很容易被体载流子掩盖. 拓扑绝缘体二维纳米结构具有超高比表面积和能带结构的可调控性, 能显著降低体态载流子的比例和凸显拓扑表面态, 并易于制备高结晶质量的单晶样品, 各种低维异质结构以及平面器件. 近年来, 我们一直致力于发展拓扑绝缘体二维纳米结构的控制生长方法和物性研究. 我们发展了拓扑绝缘体二维纳米结构的范德华外延方法, 实现了高质量大比表面积的拓扑绝缘体二维纳米结构的可控制备, 并实现了定点与定向的表面生长. 开展拓扑绝缘体二维纳米结构的谱学研究, 利用角分辨光电子能谱直接观察到拓扑绝缘体狄拉克锥形的表面电子能带结构, 发现了拉曼强度与位移随层数的依赖关系. 设计并构建拓扑绝缘体纳米结构器件, 系统研究其新奇物性, 观测到拓扑绝缘体Bi₂Se₃表面态的Aharonov-Bohm (AB)量子干涉效应等新奇量子现象, 通过栅电压实现了拓扑绝缘体纳米薄片化学势的调控, 并将拓扑绝缘体纳米结构应用于柔性透明导电薄膜. 本文首先简单介绍拓扑绝缘体的发展现状, 然后系统介绍我们开展的拓扑绝缘体二维纳米结构的范德华外延生长、谱学、电学输运特性以及透明柔性导电薄膜应用的研究, 最后对该领域所面临的机遇和挑战进行简要的展望.     

Fabrication and Application of Graphdiyne-based Heterogeneous Compositions:from the View of Interaction

Graphdiyne(GDY)has the unique feature in the topological ordered arranged sp-and sp2-hybridized carbon atoms,thus deriving a series of 2D allotropes.Due to inhomogeneous π-bonding and carbon orbital overlap between different hybrid carbon atoms,GDY possesses a natural band gap with a Dirac cones structure.And GDY exhibits semiconductor property with a conductivity of 2.516×10-4 S/m at room temperature.The topological distribution of alkyne and benzene bonds of GDY makes its surface charge distribution extremely uneven,which produces high intrinsic activity for further modification.Its unique molecular structure endows the specific interaction with various species,such as ions,atoms,molecules and nanoparticles,showing excellent charge transport capability and unique advantages in mass transfer and energy conversion.From the view of the interaction principle between GDY and different compositions,we summarized the application of GDY-based materials in the fields of catalysis,energy conversion and storage,biological detection and so on.     

MIMA—a software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements

Ion mobility spectrometry coupled to multi capillary columns (MCC/IMS) combines highly sensitive spectrometry with a rapid separation technique. MCC\IMS is widely used for biomedical breath analysis. The identification of molecules in such a complex sample necessitates a reference database. The existing IMS reference databases are still in their infancy and do not allow to actually identify all analytes. With a gas chromatograph coupled to a mass selective detector (GC/MSD) setup in parallel to a MCC/IMS instrumentation we may increase the accuracy of automatic analyte identification. To overcome the time-consuming manual evaluation and comparison of the results of both devices, we developed a software tool MIMA (MS-IMS-Mapper), which can computationally generate analyte layers for MCC/IMS spectra by using the corresponding GC/MSD data. We demonstrate the power of our method by successfully identifying the analytes of a seven-component mixture. In conclusion, the main contribution of MIMA is a fast and easy computational method for assigning analyte names to yet un-assigned signals in MCC/IMS data. We believe that this will greatly impact modern MCC/IMS-based biomarker research by “giving a name” to previously detected disease-specific molecules.     

A topological isomer of ferrocene: Theoretical approach for transition metal complexes with conjugated all trans cyclodecapentaene

We demonstrate the ability of all-trans DPEN as a suitable ligand for transition metals by DFT computation [B3LYP/6-311+G(2d,p) and BP86 level]. The iron complex Fe(DPEN) is a unique topological isomer of ferrocene.     

Duboscic acid: a potent α-glucosidase inhibitor with an unprecedented triterpenoidal carbon skeleton from Duboscia macrocarpa

Duboscic acid (1), a triterpenoid with a unique carbon backbone, was isolated from Duboscia macrocarpa Bocq. It is the first member of a new class of triterpenoids, for which the name "dubosane" is proposed. Duboscic acid has a potent α-glucosidase inhibition, and its structure was unambiguously deduced by a single-crystal X-ray diffraction study.     

Self-assembled Monolayer and Multilayer Films with Polyoxometalates on Gold Electrodes

Polyoxometalates (POMs) are a distinctive class of inorganic metal-oxygen cluster compounds which are unique in their topological and electronic versatility. They have been found applications in fields as diverse as catalysis, analysis, medicine,biochemistry,material science etc. Extensive studies of their properties are fairly important.     

无机氢化物pK_(a1)与拓扑指数~mT的关系

在Randic分子价连接性拓扑指数的基础上,构建了价电子轨道平均能量拓扑指数mT 用其0,1阶指数0T,0T和1T以及Pauling电负性差的平方分别与P区无机氢化物的pKa1值关联,拟合成3个回归方程,其相关系数分别为0.9958,0.9960和0.9965,结构选择性达到唯一性表征 预测取得了较好的结果     

Topological derivation of shape exponents for stretched exponential relaxation

In homogeneous (ideal) glasses, the important dimensionless stretched-exponential shape parameter beta is described by magic (not adjusted) simple fractions derived from fractal configuration spaces of effective dimension d* determined by different topological axioms (rules) in the presence (absence) of a forcing electric field. The rules are based on a new central principle for defining glassy states: equal a priori distributions of fractal residual configurational entropy. Our approach and its beta estimates are fully supported by the results of relaxation measurements involving many different glassy materials and probe methods. The present unique topological predictions for beta typically agree with observed values to approximately 1% and indicate that for field-forced conditions beta should be constant for appreciable ranges of such exogenous variables as temperature and ionic concentration, as indeed observed using appropriate frequency-domain data analysis. The present approach can also be inverted and used to test sample homogeneity and quality.     

Renner-Teller/Jahn-Teller intersections along the collinear axes of polyatomic molecules: C2H2 + as a case study

Recently we discussed the Renner-Teller effect in triatomic molecules [J. Chem. Phys. 125, 094102 (2006)]. In that article the main message is that the Renner-Teller phenomenon, just like the Jahn-Teller phenomenon, is a topological effect. Now we extend this study to a tetra-atomic system, namely, the C(2)H(2) (+) ion, for which topological effects are revealed when one atom surrounds the triatom axis or when two atoms surround (at a time) the two-atom axis. The present study not only supports the findings of the previous study, in particular, the crucial role played by the topological D matrix for diabatization, but it also reveals new features which are expected to be more and more pronounced the larger the original collinear molecule. As already implied, shifting away two atoms from the collinear molecular axis does not necessarily abolish the ability of the remaining two atoms to form topological effects. Moreover, the study indicates that when the two hydrogens are shifted away, the CC axis produces two kinds of topological effects: (1) a Renner-Teller effect (characterized by a topological phase of 2pi) which is revealed when the two hydrogens surround, rigidly, this axis (as mentioned above), and (2) a Jahn-Teller effect (characterized by a topological phase of pi) which is revealed when one of the hydrogens surrounds this axis while the other hydrogen is clamped to its position.     

A self-assembled fluoride-water cyclic cluster of [F(H2O)]4(4-) in a molecular box

We present an unprecedented fluoride-water cyclic cluster of [F(H(2)O)](4)(4-) assembled in a cuboid molecular box formed by two large macrocycles. Structural characterization reveals that [F(H(2)O)](4)(4-) is assembled by strong H-bonding interactions [OH···F = 2.684(3)-2.724(3) ?], where a fluoride anion plays the topological role of a water molecule in the classical cyclic water octamer. The interaction of fluoride was further confirmed by (19)F NMR and (1)H NMR spectroscopies, indicating the encapsulation of the anionic species within the cavity in solution. High-level DFT calculations and Bader topological analyses fully support the crystallographic results, demonstrating that the bonding arrangement in the fluoride-water cluster arises from the unique geometry of the host.     

Tunable Multiple Morphological Transformation of Supramolecular Hyperbranched Polymers Based on an A2B6-type POSS Monomer

The growing demands of supramolecular hyperbranched polymers integrating noncovalent interaction and unique topological structure merits had received considerable interest in the fabrication of novel materials for advanced applications.Herein,we prepared A2B6-type POSS-containing supramolecular hyperbranched polymers with multiple morphologies including lamellar-like,branched,hollow,core-shell and porous spherical structures through regulating self-assembling monomer concentrations and solvent polarities.The incorporation of appropriate emulative guest molecules would further trigger morphological transformations (such as vesicles and spherical micelles) by synergistic effects of unique POSS aggregation ability,supramolecular complexations and hydrophilic-hydrophobic interactions.Thus,this facile and universal strategy may enable a modular nanofabrication of supramolecular hyperbranched polymers with diversiform topological structure and sophisticated multifunctionality for their potential applications.