The de novo design of median molecules within a property range of interest

Summary In this paper an application is presented of the median molecule workflow to the de novo design of novel molecular entities with a property profile of interest. Median molecules are structures that are optimised to be similar to a set of existing molecules of interest as an approach for lead exploration and hopping. An overview of this workflow is provided together with an example of an instance using the similarity to camphor and menthol as objectives. The methodology of the experiments is defined and the workflow is applied to designing novel molecules for two physical property datasets: mean molecular polarisability and aqueous solubility. This paper concludes with a discussion of the characteristics of this method.     

On the Permanental Polynomials of Some Graphs

Let G be a simple graph with adjacency matrix A(G) and (G,x) the permanental polynomial of G. Let G × H denotes the Cartesian product of graphs G and H. Inspired by Kleins idea to compute the permanent of some matrices (Mol. Phy. 31 (3) (1976) 811–823), in this paper in terms of some orientation of graphs we study the permanental polynomial of a type of graphs. Here are some of our main results.1.If G is a bipartite graph containing no subgraph which is an even subdivision of K _2,3, then G has an orientation G ^e such that (G,x) = det (xI-A(G ^e )), where A(G ^e ) denotes the skew adjacency matrix of G ^e.2.Let G be a 2-connected outerplanar bipartite graph with n vertices. Then there exists a 2-connected outerplanar bipartite graph with 2n+2 vertices such that (G,x) is a factor of .3.Let T be an arbitrary tree with n vertices. Then , where ₁ , ₂ , ..., _n are the eigenvalues of T.     

Pattern of separatrices and intrinsic reaction coordinates for degenerate thermal rearrangements

A structurally stable model of the standard adiabatic gradient field of the potential energy surface for certain pericyclic reactions is derived.These reactions are not subjected to the principles of orbital isomerism or to the Woodward-Hoffmann rules.Use is made of a principle established by Ariel Fernández and Oktay Sinanolu which precludes direct meta-IRC connections between transition states.It is shown that Jahn-Teller isomers of the singlet biradicals involved in the process are not interconvertible since the biradical configuration is not a transition state but a critical point with Hessian matrix with two negative eigenvalues.The topological features of the PES obtained by combinatorial methods are in full agreement with earlier results obtained from MINDO calculations.     

Note on the application of the reduced graph model in conjunction with search trees to the enumeration ofKekulé structures

The reduced graph model, when used in conjunction with the search trees method, provides a novel combinatorial procedure for the enumeration and generation ofKekulé structures. The procedure is suited for large benzenoid hydrocarbons consisting of cata- and thin peri-condensed parts.

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Zur Anwendung des Reduced Graph Model im Zusammenhang mit Search Trees zur Ermittlung der Anzahl möglicherKekulé-Strukturen

Zusammenfassung Das Modell erlaubt mit der im Titel genannten Kombination eine neuartige Methode zur Ermittlung und Generierung vonKekulé-Strukturen. Das Verfahren ist für große benzoide Kohlenwasserstoffe geeignet, die aus cata- und (dünnen) peri-kondensierten Teilstrukturen bestehen.

     

A novel nomenclature of polycyclic aromatic hydrocarbons without using graph centre

In this paper, we develop a novel adjacency matrix, He-matrix, corresponding to the dualist graph. Without using the graph center concept, we advance a novel nomenclature of polycyclic aromatic hydrocarbons. Further, we derive some distinguishing theorems about PAH molecules and present some results of our automatic derivatization and automatic classification counting of fused PAH molecules.     

直键与弯键的对称性判据

一穹键的提出人们认为,杂化轨道(HAO)角函数的最大值方向(亦即HAO的方向)指向与之键合的原子,这样形成的化学键称为“直键”。但环丙烷分子中的三个碳原子构成三元环,有60°的键角。而任意两个正交的S-P杂化轨道之间的夹角θ都不可能小于90°,因而形成C-C键的HAO,不可能指向键合原子,环上的C-C键不可能是直键,而是“弯键”(BentBond)。通常,人们认为张力分子环上的键是弯键,其他的键为直键。     

Mathematical studies of Kekulé structures

The perfect matching vector and forcing and the Kekulé-vector of cata-benzenoids are defined. Two theorems are given which set the sufficient and necessary conditions for HKZ-vector (Harary et al. J Math Chem 6:295, 1991) and Kekulé-vector in cata-benzenoids. Additional two theorems are obtained which give sharp bounds for the modules of HKZ- and Kekulé vectors. Dedicated to Professor Tadeusz Marek Krygowski on the happy occasion of his 70th birthday.     

On the Randić Index of Acyclic Conjugated Molecules

The Randić index of an organic molecule whose molecular graph is G is the sum of the weights (d(u)d(v))^−1/2 of all edges uv of G, where d(u) and d(v) are the degrees of the vertices u and v in G. We give a sharp lower bound on the Randić index of conjugated trees (trees with a perfect matching) in terms of the number of vertices. A sharp lower bound on the Randić index of trees with a given size of matching is also given Mei Lu: Partially supported by NNSFC (No. 60172005) Lian-zhu Zhang: Partially supported by NNSFC (No. 10271105) Feng Tian: Partially supported by NNSFC (No. 10431020)     

Cyclic Conjugation Energy Effects in Polycyclic π-Electron Systems

Summary. The fact that cyclic arrangements of double bonds have a dramatic effect on the behavior of conjugated organic molecules is known since the 19th century. The fact that in monocyclic conjugated systems the size of the cycle and the number of -electrons involved is decisive for their stability (aromaticity) or lack of stability (antiaromaticity) is known since the 1930s. In polycyclic -electron systems several cyclic effects are present simultaneously and their separation became possible only recently. A molecular orbital method has been elaborated, by means of which the energy effects of individual cycles in polycyclic -electron systems can be estimated. This method is briefly outlined and illustrated by pertinent examples. An exhaustive bibliography of the topic considered is given.     

Theoretical study on the structure and property relationship of the cationic conjugated polyelectrolytes

A theoretical study using density functional theory was performed to understand the structure/property relationship of the cationic conjugated polyelectrolytes, poly[9,9-bis-(6′-N,N,N-trimethylammonium) hexyl] fluorene-alt-4,7-(2,1,3-benzothiadiazole)] (PFBT-X, where X = Br). The torsion angle between the fluorene and benzothiadiazole units in the PFBT monomer was found to substantially affect the structural and electronic properties of the cationic PFBT monomer. The changes of geometrical parameter, HOMO and LUMO energy levels, and band gap, as well as the absorption maximum are discussed in terms of the torsion in the PFBT monomer structure. For comparison, its neutral analogue, the monomer of poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) (F8BT) was also studied. The length of conjugation backbone was also examined.