Novel shape descriptors for molecular graphs.

We report on novel graph theoretical indices which are sensitive to the shapes of molecular graphs. In contrast to the Kier's kappa shape indices which were based on a comparison of a molecular graph with graphs representing the extreme shapes, the linear graph and the "star" graph, the new shape indices are obtained by considering for all atoms the number of paths and the number of walks within a graph and then making the quotients of the number of paths and the number of walks the same length. The new shape indices show much higher discrimination among isomers when compared to the kappa shape indices. We report the new shape indices for smaller alkanes and several cyclic structures and illustrate their use in structure-property correlations. The new indices offer regressions of high quality for diverse physicochemical properties of octanes. They also have lead to a novel classification of physicochemical properties of alkanes.     

Computing a new family of shape descriptors for protein structures

The large-scale 3D structure of a protein can be represented by the polygonal curve through the carbon alpha atoms of the protein backbone. We introduce an algorithm for computing the average number of times that a given configuration of crossings on such polygonal curves is seen, the average being taken over all directions in space. Hereby, we introduce a new family of global geometric measures of protein structures, which we compare with the so-called generalized Gauss integrals.     

Quantum molecular similarity. 3. QTMS descriptors.

Building on the ideas of a previous paper [part 1, J. Phys. Chem. A 1999, 103, 2883] we present a new molecular similarity method based on the topology of the electron density. This method is directly applicable to QSARs and is called quantum topological molecular similarity (QTMS). It has been tested for five sets of carboxylic systems including para- and meta-benzoic acid, para-phenylacetic acid, 4-X-bicyclo[2.2.2]octane-1-carboxylic acids, and polysubstituted benzoic acids. In combination with the partial least squares (PLS) procedure QTMS is able to produce excellent and statistically valid regressions. It is shown that QTMS avoids certain challenges of traditional Carbó-like similarity indices. Finally, QTMS is able to suggest a molecular fragment that contains the active center or the part of the molecule that is responsible for the QSAR.     

Structure and electronic properties of ladder polymers. A new class of conducting polymers

Theoretical calculations have been applied to design novel synthetic polymers which show metallic conductivity without doping. Some selected highly conjugated structures were calculated using a HUCKELMO method extended by introducing elastic sigma bonds. A group of highly conjugated aromatic ladder polymers is promising in this context. Another interesting group consists of laddered heteroaromatic structures in which carbon atoms are replaced by nitrogen. Ionization potentials, electron affinities, band widths, band gaps as well as oxidation and reduction potentials were calculated. Small, band gaps were obtained for polyacene, polyperinaphthalene and polypyridinopyridine. The values are in good aggreement with that obtained on the basis of the VEH method. This paper reports also some efforts to prepare polyacene, polyperinaphthalene and polypyridinopyridine, and to investigate their electronic properties. Concerning their electrochemical properties high specific capacities and good electrochemical stability has been found in aprotic lithium cells.     

Probing molecular shape. 1. Conformational studies of 5-hydroxyhexahydropyrimidine and related compounds

Understanding the factors that determine molecular shape enables scientists to begin to understand and tailor molecular properties and reactivity. Many biomolecules and bioactive compounds contain aliphatic heterocyclic rings whose conformations play a major role in their biological activity. The interplay of a number of factors, both steric and electronic, is examined for 5-hydroxyhexahydropyrimidine (1) and related compounds with use of spectroscopy and molecular modeling.