A graph-theoretic approach to quantitative structure—activity/reactivity studies

Characterization of molecular species based on the use of suitable graph invariants (graph paths, in particular) can provide a quantitative means of encoding structure; the technique is complementary to commoner approaches to studies of quantitative structure— activity relationships. Graph path encoding is here applied to quantitative studies of relationships between molecular structures and biological activity; the examples are the rates of various substrate reactions with hexoldnase, and the potential opiate-like activity of enkephalin analogs.     

Hybridization in some macrocyclic polyacetylenes

The hybridization in several cyclic polyacetylene compounds has been calculated by the maximum overlap method, assuming planar and non-planar geometries of the molecules. In the planar configuration the hybrids describing the molecular skeleton deviate from the corresponding bond directions. We have a few “bent” bonds, but in contrast to the situation in small rings, here the deviation angles are negative, i.e., the hybrids point toward the inside of the ring. Non-planar structures in which acetylene groups are kept in a plane and CCH₂ or CH₂ groups are displaced out of the plane show less deviation from the bond directions of bent bonds. Furthermore, the deviation angles decrease with an increase in the out-of-plane displacement of methylene groups. Finally, when the angle of bending of the molecules approaches 50°, the deviation vanishes, predicting a puckered conformation for the molecules. Correlation between CC stretching vibration frequencies and the corresponding CC bond overlap is discussed.     

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.     

Algebraic Kekulé structures of benzenoid hydrocarbons

An algebraic Kekulé structure of a benzenoid hydrocarbon is obtained from an ordinary Kekulé structure by inscribing into each hexagon the number of pi-electrons which (according to this Kekulé structure) belong to this hexagon. We show that in the case of catafusenes, there is a one-to-one correspondence between ordinary and algebraic Kekulé structures. On the other hand, in the case of perifusenes, one algebraic Kekulé structure may correspond to several ordinary Kekulé structures.     

On the evaluation of the characteristic polynomial via symmetric function theory

The use of power sum symmetric functions leads to Newton's identities, which relate the traces of various powers ofA, the adjacency matrix of a graph, and the coefficients of the characteristic polynomials. While it is possible to solve Newton's identities and generate the coefficients by recursion or, alternatively, to derive them by sequential manipulations (yielding the explicit formulas), we show how the results can be expressed using a combinatorial approach and relate the evaluation of the coefficients to selected Young diagrams.     

Novel characterization of proteomics maps by sequential neighborhoods of protein spots

We consider a characterization of proteomics maps based on an alternative kind of neighborhood graphs for the protein spots on 2-D gel. The novel approach considers for every protein spot only the nearest neighborhood consisting of protein spots of higher abundance. The approach has the simplicity and advantages of the recently introduced characterization of proteome maps based on considering the nearest neighborhoods of protein spots, but it also has important additional desirable computational features. The characterization of the nearest neighborhood graphs of 2-D gel proteomics maps is sensitive to the number of spots considered and may lead to changes in the degree of similarity of different maps when the number of points has been changed, thus imposing restrictions on the protocol used for comparison of maps. The novel approach presented in this work is less sensitive to the number of points used in the analysis because graphs are constructed in a stepwise process in which the role of more distant neighbors has been diminished by linking a new spot to the nearest spot that has been already part of the neighborhood graph. In this way a graph with N + 1 spots is obtained from the graph on N spots by adding a single new link, while in the case of the nearest neighborhood graphs adding a new spot introduces novel neighborhoods and generally results in a graph that may differ significantly from the neighborhood graph on N points.     

On the characterization of local aromatic properties in benzenoid hydrocarbons

A generalization of the Kekulé index for composite valence structures provides a quantitative value corresponding to Clar's assessment of benzenoid character of aromatic ring systems. The idea involved is further specialized for the individual local rings in the molecules. Comparison with limited experimental data supports the validity of this approach.     

Spectral representation of reduced protein models

We consider a spectrum-like two-dimensional graphical representation of proteins based on a reduced protein model in which 20 amino acids are grouped into five classes. This particular grouping of amino acids was suggested by Riddle and co-workers in 1997. The graphical representation is based on depicting sequentially the amino acids on five horizontal lines at equal separations. One-letter codes, B, O, U, X and Y, to which numerical values 1 to 5 have been assigned, are suggested as labels for the fictional amino acids that represent all the amino acids within each group. The approach is illustrated on ND6 proteins of eight species having from 168 to 175 amino acids. While visual inspection of the novel spectral graphical representations of proteins may reveal local similarities and dissimilarities of protein sequences, arithmetic manipulations of spectra offer an elegant route to graphic visualization of the degree of similarity for selected pairs of proteins.