Property correlations for chlorofluoro carbons and alternatives using structural parameters

Because of their wide ranging applications, the properties of chlorofluoro carbons (CFCs) and their alternatives are studied and correlated in terms of the parameters derived from molecular structures. The properties correlated are of physical, thermodynamic and transport in nature. The input parameters include molar refraction (R _M), molecular connectivity (χ) and van der Waals equation coefficients (a and b), all of which are easily estimated from molecular structures. The correlations developed for the 11 properties studied showed average absolute deviations ranging between 3.5% and 13.7%. The correlation coefficients calculated for the equations developed ranged between 0.9557 and 0.9921.     

The overall Wiener index--a new tool for characterization of molecular topology.

Recently, the concept of overall connectivity of a graph G, TC(G), was introduced as the sum of vertex degrees of all subgraphs of G. The approach of more detailed characterization of molecular topology by accounting for all substructures is extended here to the concept of overall distance OW(G) of a graph G, defined as the sum of distances in all subgraphs of G, as well as the sum of eth-order terms, (e)OW(G), with e being the number of edges in the subgraph. Analytical expressions are presented for OW(G) of several basic classes of graphs. The overall distance is analyzed as a measure of topological complexity in acyclic and cyclic structures. The potential usefulness of the components of this generalized Wiener index in QSPR/QSAR is evaluated by its correlation with a number of properties of C3-C8 alkanes and by a favorable comparison with models based on molecular connectivity indices.     

Anisotropy of the van der Waals Configuration of Atoms in Complex,Condensed, and Gas-Phase Molecules

Anisotropic van der Waals (vdW) radii of 5b–7bsubgroup elements were determined from structures of gas-phase van der Waals complexes and crystal molecular compounds. The anisotropy of the van der Waals configuration of atoms was shown to decrease when going from isolated molecules to the condensed state. Variations in intermolecular distances, which are usually explained in terms of the formation of hydrogen bonds, are substantially governed by the anisotropic effect.     

GTI-space: the space of generalized topological indices

A new extension of the generalized topological indices (GTI) approach is carried out to represent “simple” and “composite” topological indices (TIs) in an unified way. This approach defines a GTI-space from which both simple and composite TIs represent particular subspaces. Accordingly, simple TIs such as Wiener, Balaban, Zagreb, Harary and Randić connectivity indices are expressed by means of the same GTI representation introduced for composite TIs such as hyper-Wiener, molecular topological index (MTI), Gutman index and reverse MTI. Using GTI-space approach we easily identify mathematical relations between some composite and simple indices, such as the relationship between hyper-Wiener and Wiener index and the relation between MTI and first Zagreb index. The relation of the GTI-space with the sub-structural cluster expansion of property/activity is also analysed and some routes for the applications of this approach to QSPR/QSAR are also given.     

拓扑指数与烷烃色谱保留指数的定量相关研究

基于分子图论, 计算了64个链烷烃的一阶连接性指数(¹χ)和奇偶指数(OEI), 并对气相色谱保留指数进行定量结构-性质相关(QSPR)研究, 得到多元线性回归模型RI＝55.7631＋25.7317OEI＋111.4508¹χ (R²＝0.9960, RMS＝9.36, ARD＝1.02%). 交叉验证和预测结果表明, 所建立的QSPR模型具有良好的稳定性和预测能力. 与文献结果比较, 本文所用的参数少, 且计算简便.     

Integration of Graph Theory and Quantum Chemistry for Structure-Activity Relationships

Abstract

The objective of this article is to outline both graph-theoretically based and quantum chemically based structural indices of potential use in quantitative structure activity correlations. We consider graph-theoretical indices such as the connectivity index, topological index, Wiener index and molecular ID indices. Several structural and geometry-dependent indices can be derived from semiempirical and ab initio quantum calculations based on the charge densities, overlap matrices, frontier orbitals, molecular hardness, free valence, density matrices, quantum spectral difference indices, quantum spectral indices and bond matrices. Finally, the use of electrostatic potentials and charge densities for the prediction of reactive sites will be discussed.     

Condensed Extended Hyper-Wiener Index

According to the definitions of molecular connectivity and hyper-Wiener index, a novel set of hyper-Wiener indexes （Dn, ^mDn） were defined and named as condensed extended hyper-Wiener index, the potential usefulness of which in QSAR/QSPR is evaluated by its correlation with a number of C3-C8 alkanes as well as by a favorable comparison with models based on molecular connectivity index and overall Wiener index.     

Semi-empirical topological index: development of QSPR/QSRR and optimization for alkylbenzenes

The semi-empirical topological index, I(ET), was developed and optimized to describe the chromatographic retention of alkylbenzenes on the squalane stationary phase. The simple linear regression between the chromatographic retention and the proposed index, for 122 alkylbenzenes studied, is of good quality (determination coefficient, r(2)=0.9996, standard deviation, S.D.=5.5, and leave-one-out cross-validation correlation coefficient, r(CV)(2)=0.9996). The predictive ability of I(ET) was also verified for stationary phases with two different polarities (SE-30 and Carbowax 20 M), and good results were obtained, especially for the stationary phase with low polarity, showing that the specific molecular interactions occur on highly polar phases. The I(ET) was applied to construct quantitative structure-property relationship (QSPR) models for representative properties such as boiling point, Bp(degrees C), octanol/water partition coefficient, log P, van der Waals volume (V(W)) and molar refractivity (R(M)). Satisfactory quality QSPR models were obtained with Bp, V(W) and R(M) showing that the molecular size and dispersive forces are dominating factors with respect to the chromatographic retention.     

Different van der Waals radii for organic and inorganic halogen atoms: a significant improvement in IMOMM performance

The discrepancies between X-ray and integrated molecular orbital molecular mechanics computed geometries for Os(H)₂Cl₂(PⁱPr₃)₂ and Ir(H)₂Cl(P^tBu₂ Ph)₂ are explained by the inadequacy of the default molecular mechanics van der Waals radii for halogen elements. A simple procedure is proposed for the calculation of corrected van der Waals radii, and the application of the corrected radius for chloride is shown to improve substantially the results for the systems under test. Received: 25 February 1997 / Accepted: 7 April 1997     

The (n,n)-graphs with the first three extremal Wiener indices

Let G = (V, E) be a simple connected graph with vertex set V and edge set E. The Wiener index W(G) of G is the sum of distances between all pairs of vertices in G, i.e., , where d _G (u, v) is the distance between vertices u and v in G. In this paper, we first give a new formula for calculating the Wiener index of an (n,n)-graph according its structure, and then characterize the (n,n)-graphs with the first three smallest and largest Wiener indices by this formula.     

Molecular Modeling for Mobile Phase Optimization in RP-HPLC

Abstract

The applicability of molecular parameters calculated on the bases of molecular mechanics have been investigated for the prediction of reversed-phase retention behavior of structurally unrelated series of drug molecules. Non-polar, non-polar unsaturated and polar surface areas, surface energies, dipole moments, van der Waals radii and hydrophobicity values expressed by the logarithm of the octanol/water partition coefficients have been calculated from the molecular structure. The reversed-phase retention behavior was described by the slope and the intercept of the straight lines obtained by plotting the log k¹ values against the acetonitrile concentration of the mobile phase. The acetonitrile concentration (OP%₀) which was needed for the log k¹ = 0 retention was also calculated from the slope and intercept values. Step-wise linear regression analyses have been applied for revealing the correlations between the investigated parameters. The slope values could be described by the difference of the non-polar and non-polar accessible surface areas or by the total surface energy values and the van der Waals radii. The intercept values could be described by the hydrophobicity parameter, the slope and the reciprocal values of dipole moment. The acetonitrile concentration for the log k'=O retention (OP%₀) could have been calculated from the hydrophobicity and the non-polar unsaturated surface area values of the investigated compounds.     

Resonances of triatomic van der Waals molecules by the complex discrete variable representation

Summary The results of Light and co-workers [J. Chem. Phys. 85:4594 (1986); 86:3065 (1987); 92:2129 (1990)] for the Hamiltonian matrix of a triatomic van der Waals molecule in the discrete variable representation, DVR, is extended to complex-scaled Hamiltonians. As an illustrative numerical example theJ=1 resonances positions and widths of a van der Waals model system were obtained by the calculation of the complex-scaled Hamiltonian matrix in the DVR formalism.Supported in part by the Albert Einstein Research Fund, and the Fund for the Promotion of Research at the Technion     

Ionic Liquids: Dissecting the Enthalpies of Vaporization

We calculate the heats of vaporisation for imidazolium‐based ionic liquids [C_nmim][NTf₂] with n=1, 2, 4, 6, 8 by means of molecular dynamics (MD) simulations and discuss their behavior with respect to temperature and the alkyl chain length. We use a force field developed recently. The different cohesive energies contributing to the overall heats of vaporisations are discussed in detail. With increasing alkyl chain length, the Coulomb contribution to the heat of vaporisation remains constant at around 80 kJ mol^?1, whereas the van der Waals interaction increases continuously. The calculated increase of about 4.7 kJ mol^?1 per CH₂‐group of the van der Waals contribution in the ionic liquid exactly coincides with the increase in the heats of vaporisation for n‐alcohols and n‐alkanes, respectively. The results support the importance of van der Waals interactions even in systems completely composed of ions.     

A comparative QSAR study using Wiener, Szeged, and molecular connectivity indices

In this study we have investigated the relative correlation potential of Wiener (W), Szeged (Sz), and molecular connectivity indices (0chiR, 1chiR and 2chiR) in developing quantitative structure-activity relationships, QSAR; log P values of benzoic acid and its nuclear-substituted derivatives were used for this purpose. The statistical analyses for univariate and multivariate correlations had indicated that both W and Sz are closely related to the connectivity indices (mchiR) and that the W, the Sz, and the 1chiR indices have similar modeling potentials. 1chiR gives slightly better results than both W and Sz. Other connectivity indices 0chiR and 2chiR correlate poorly with log P.