Application of variable anti-connectivity index to active sites. Modelling pK(a) values of aliphatic monocarboxylic acids.

A partial distance-weighted variable anti-connectivity topological index was introduced for modelling pK(a) values of 31 aliphatic carboxylic acids and haloalkyl-carboxylic acids. The partial distance-weighted variable anti-connectivity index showed superior modelling capabilities compared with the index calculated from the complete graph, because it is capable of accounting correctly for the intramolecular interactions of unconnected vertices to specific bond strengths (active site), thereby improving the RMS(CV) error by about 30% (0.221 pK(a) units).

Complexity of chemical graphs in terms of size, branching, and cyclicity.

Chemical graph complexity depends on many factors, but the main ones are size, branching, and cyclicity. Some molecular descriptors embrace together all these three parameters, which cannot then be disentangled. The topological index J (and its refinements that include accounting for bond multiplicity and the presence of heteroatoms) was designed to compensate in a significant measure for graph size and cyclicity, and therefore it contains information mainly on branching. In order to separate these factors, two new indices (F and G) related with J are proposed, which allow to group together graphs with the same size into families of constitutional formulas differing in their branching and cyclicity. A comparison with other topological indices revealed that a few other topological indices vary similarly with index G, notably DN2S4 among the triplet indices, and TOTOP among the indices contained in the Molconn-Z program. This comparison involved all possible chemical graphs (i.e. connected planar graphs with vertex degrees not higher than four) with four through six vertices, and all possible alkanes with four through nine carbon atoms.

Using protochirons for three-dimensional coding of certain chemical structures.

For three-dimensional coding (including enantiomerism) of staggered paths and circuits on the diamond lattice, or paths/circuits with angles 90 degrees or 180 degrees on the cubic lattice, use is made of the previously defined paths-3 (paths of length three bonds defining two intersecting planes). The two cases mentioned above are examined and exemplified. In the diamond lattice there are three kinds of diamond-paths-3: one is achiral (Z) and two are chiral and enantiomeric (R and S). In the cubic lattice there are six kinds of orthopaths-3, of which only two are chiral and enantiomeric (R and S) and four are achiral (I, L, U, and Z). The chiral paths-3 are the previously defined protochirons in the respective lattice. Coding ascribes to each bond the letter that would characterize it if it were the central bond of an isolated path-3. To obtain a unique code out of several equally correct ones it is proposed to use the convention of inverse alphabetic priority in the above system of letters.

On structural interpretation of several distance related topological indices.

We consider the role that individual bonds play in bond-additivities in order to better understand the structural basis of various topological indices. In particular we consider indices closely related to the Wiener index (W) and the distance matrix and search for optimal weights of terminal and interior CC bonds in alkanes for a selection of physicochemical properties. It is interesting to note that different properties are associated with different relative roles of the exterior and the interior CC bonds.

Wiener index extension by counting even/odd graph distances.

Chemical structures of organic compounds are characterized numerically by a variety of structural descriptors, one of the earliest and most widely used being the Wiener index W, derived from the interatomic distances in a molecular graph. Extensive use of such structural descriptors or topological indices has been made in drug design, screening of chemical databases, and similarity and diversity assessment. A new set of topological indices is introduced representing a partitioning of the Wiener index based on counts of even and odd molecular graph distances. These new indices are further generalized by weighting exponents which can be optimized during the quantitative structure-activity/-property relationship (QSAR/QSPR) modeling process. These novel topological indices are tested in QSPR models for the boiling temperature, molar heat capacity, standard Gibbs energy of formation, vaporization enthalpy, refractive index, and density of alkanes. In many cases, the even/odd distance indices proposed here give notably improved correlations.

Prediction of mutagenicity of aromatic and heteroaromatic amines from structure: a hierarchical QSAR approach.

Due to the lack of experimental data, there has been increasing use of theoretical structural descriptors in the hazard assessment of chemicals. We have used a hierarchical approach to develop class-specific quantitative structure-activity relationship (QSAR) models for the prediction of mutagenicity of a set of 95 aromatic and heteroaromatic amines. The hierarchical approach begins with the simplest molecular descriptors, the topostructural, which encode limited chemical information. The complexity is then increased, adding topochemical, geometric, and finally quantum chemical parameters. We have also added log P to the set of independent variables. The results indicate that the topological parameters, i.e., the topostructural and topochemical indices, explain the majority of the variance, and that the inclusion of log P, geometric, and quantum chemical parameters does not result in significantly improved predictive models.

Quantitative structure-retention relationships for gas chromatographic retention indices of alkylbenzenes with molecular graph descriptors.

Quantitative structure-retention relationships (QSRR) represent statistical models that quantify the connection between the molecular structure and the chromatographic retention indices of organic compounds, allowing the prediction of retention indices of novel, not yet synthesized compounds, solely from their structural descriptors. Using multiple linear regression, QSRR models for the gas chromatographic Kováts retention indices of 129 alkylbenzenes are generated using molecular graph descriptors. The correlational ability of structural descriptors computed from 10 molecular matrices is investigated, showing that the novel reciprocal matrices give numerical indices with improved correlational ability. A QSRR equation with 5 graph descriptors gives the best calibration and prediction results, demonstrating the usefulness of the molecular graph descriptors in modeling chromatographic retention parameters. The sequential orthogonalization of descriptors suggests simpler QSRR models by eliminating redundant structural information.

Modeling the anticarcinogenic action of retinoids by making use of the OASIS method. 3. Inhibition of the induction of ornithine decarboxylase by arotinoids.

A series of 15 congeneric aromatic retinoids (arotinoids) was subjected to a study of the conformational dependence of basic molecular descriptors, and the anticarcinogenic potency of the compounds was modeled by the sophisticated OASIS (optimized approach based on structural indices set) method. A high correlation was obtained for both two-variable models and three-variable models. The best models of these two kinds had correlation coefficients of 0.956 vs 0.988 and standard deviations s2 = 0.14 vs 0.04, respectively. The most significant variables were several interatomic and topological distances, which specify the optimum geometric drug-receptor fit. The group of significant electronic descriptors included characteristic pi-bond orders, the electronic charge at one atomic position in the tetrahydronaphthalene ring, the total electronic energy, and two electronic-topological indices. An electrostatic drug-receptor interaction was conjectured on this basis. A contribution of the through-cell membrane transport was inferred from the importance of molecular refraction in the best three-variable model. The models derived were validated by the leave-one-out procedure and by reproducing the activities of five arotinoids not included in the correlation sample.

Carbonic anhydrase activators. VII. Isozyme II activation by bisazolyl-methanes, -ethanes and related azoles.

A correlation was found between the carbonic anhydrase II activating power and the pKa values for a series of azoles, bisazolylmethanes and bisazolylethanes. Strong activations were found for compounds with pKa's in the interval 6.5-8.0. The mechanism of action for such activators is discussed.

Reaction of pyrylium salts with nucleophiles. 23: triarylethene derivatives containing an oxyalkyleneamino or oxyalkylene-N-pyridinium side chain.

A synthetic design was devised for preparing primary amines related to anticancer drugs clomiphene and tamoxifen on the basis of key intermediates with a phenolic group, to which a side chain (omega-aminoethoxy or omega-aminopropoxy) was attached. These compounds were then reacted with 2,4,6-trimethyl- or 2,4,6-triphenylpyrylium salts. This afforded pyridinium analogues of clomiphene and tamoxifen as potential therapeutic agents for treatment against hormone-dependent tumors.

Modeling the anticancer action of some retinoid compounds by making use of the OASIS method.

The powerful OASIS (optimized approach based on structural indices set) approach is applied to the anticancer activity of a series of vitamin A analogs. The best three- and four-variable models obtained via the OASIS technique have correlation coefficients of 0.973 vs. 0.990 and standard deviations s2 = 0.11 and 0.05, respectively. The models incorporate the hydrophobicity factor log P, two geometric parameters (topological indices and/or 3-D steric ones), and the molecular dipole moment. For a set of 15 compounds studied here, the activity measured by ED50 was well correlated by models with approximately equal contribution of the through cell membrane transport and the geometric drug-receptor correspondence while weak nonspecific electronic interaction was also found to play some role. Comparison to previous treatments of this data is given and extension to larger sets is discussed.

Carbonic anhydrase inhibitors. V: Pyrylium salts in the synthesis of isozyme-specific inhibitors.

Syntheses and physicochemical properties of 2,4,6-tri-, 2,3,4,6-tetra-, or 2,3,4,5,6-pentasubstituted 1-(2-sulfonamido-1,3,4-thiadiazol-5-yl)pyridinium perchlorates are presented. The new compounds, putative inhibitors of membrane-bound carbonic anhydrase, were tested for inhibitory action on the bovine red cell enzyme.

Hypothetical strain-free oligoradicals.

Several new classes of oligoradicals free of angle strain are suggested and examined by means of molecular orbital calculations. The collapse products of these hypothetical radicals are highly strained molecules. Various electronic strategies for the stabilization of these oligoradicals have been explored.