Applications of caterpillar trees in chemistry and physics

The relations of caterpillar trees (which are also known as Gutman trees and benzenoid trees) to other mathematical objects such as polyhex graphs, Clar graphs, king polyominos, rook boards and Young diagrams are discussed. Potential uses of such trees in data reduction, computational graph theory, and in the ordering of graphs are considered. Combinatorial and physical properties of benzenoid hydrocarbons can be studied via related caterpillars. It thus becomes possible to study the properties of large graphs such as benzenoid (i.e. polyhex) graphs in terms of much smaller tree graphs. Generation of the cyclic structures of wreath and generalized wreath product groups through the use of caterpillar trees is illustrated.     

Quest for molecular graphs with maximal energy: a computer experiment

If lambda(1), lambda(2),..., lambda(n) are the eigenvalues of a graph G, then the energy of G is defined as E(G) = the absolute value of lambda(1) + the absolute value of lambda(2) +.... + the absolute value of lambda(n). If G is a molecular graph, representing a conjugated hydrocarbon, then E(G) is closely related to the respective total pi-electron energy. It is not known which molecular graph with n vertices has maximal energy. With the exception of m = n - 1 and m = n, it is not known which molecular graph with n vertices and m edges has maximal energy. To come closer to the solution of this problem, and continuing an earlier study (J. Chem. Inf. Comput. Sci. 1999, 39, 984-996, ref 7), we performed a Monte Carlo-type construction of molecular (n,m)-graphs, recording those with the largest (not necessarily maximal possible) energy. The results of our search indicate that for even n the maximal-energy molecular graphs might be those possessing as many as possible six-membered cycles; for odd n such graphs seem to prefer both six- and five-membered cycles.     

Semi-cartesian product of graphs

In this paper, we define a kind of new product graphs with hexagonal inner faces, called semi-cartesian products, so that they directly link with hexagonal system, e.g., the semi-cartesian product of an even cycle and a path is a zigzag polyhex nanotube, a path and an even cycle is an armchair polyhex nanotube, two even cycles is a polyhex nanotorus and two paths is a polyhex lattice. Then we consider the distance in a semi-cartesian product and show two formulas to calculate the distance of two vertices and the sum of all pair of distances. Moreover we illustrate that the applying of the semi-cartesian products would be greatly simplifies the calculation of the distances in the carbon nanotubes and polyhex nanotorus by presenting some examples.     

Graph-theoretical analysis of the clar's aromatic sextet : Mathematical properties of the set of the kekulé patterns and the sextet polynomial for polycyclic aromatic hydrocarbons

The mathematical structure of a set of the Kekulé patterns for a polycyclic aromatic hydrocarbon has been analysed graph-theoretically. By defining the proper and improper sextets, sextet pattern, Clar transformation, and sextet rotation, one can prove the important property of the sextet polynomial B_G(x) as B_G(1) = K(G), where K(G) is the number of the Kekulé patterns for thin polyhex graph G. For fat polyhex graphs such as coronene the above relation is found to be also valid by introducing the concept of a super sextet. All the Kekule patterns for a given G are shown to form a hierarchical tree structure by the sextet rotation. The theory developed in this paper gives a mathematical basis and interpretation for the concept of the Clar's aromatic sextet.     

On the centrality of vertices of molecular graphs

For acyclic systems the center of a graph has been known to be either a single vertex of two adjacent vertices, that is, an edge. It has not been quite clear how to extend the concept of graph center to polycyclic systems. Several approaches to the graph center of molecular graphs of polycyclic graphs have been proposed in the literature. In most cases alternative approaches, however, while being apparently equally plausible, gave the same results for many molecules, but occasionally they differ in their characterization of molecular center. In order to reduce the number of vertices that would qualify as forming the center of the graph, a hierarchy of rules have been considered in the search for graph centers. We reconsidered the problem of “the center of a graph” by using a novel concept of graph theory, the vertex “weights,” defined by counting the number of pairs of vertices at the same distance from the vertex considered. This approach gives often the same results for graph centers of acyclic graphs as the standard definition of graph center based on vertex eccentricities. However, in some cases when two nonequivalent vertices have been found as graph center, the novel approach can discriminate between the two. The same approach applies to cyclic graphs without additional rules to locate the vertex or vertices forming the center of polycyclic graphs, vertices referred to as central vertices of a graph. In addition, the novel vertex “weights,” in the case of acyclic, cyclic, and polycyclic graphs can be interpreted as vertex centralities, a measure for how close or distant vertices are from the center or central vertices of the graph. Besides illustrating the centralities of a number of smaller polycyclic graphs, we also report on several acyclic graphs showing the same centrality values of their vertices. © 2013 Wiley Periodicals, Inc.     

From symmetry-labeled quotient graphs of crystal nets to coordination sequences

The combinatorial topology of crystal structures may be described by finite graphs, called symmetry-labeled quotient graphs or voltage graphs, with edges labeled by symmetry operations from their space group. These symmetry operations themselves generate a space group which is generally a non-trivial subgroup of the crystal space group. The method is an extension of the so-called vector method, where translation symmetries are used as vector labels (voltages) for the edges of the graph. Non-translational symmetry operations may be used as voltages if they act freely on the net underlying the crystal structure. This extension provides a significant reduction of the size of the quotient graph. A few uninodal and binodal nets are examined as illustrations. In particular, various uninodal nets appear to be isomorphic to Cayley color graphs of space group. As an application, the full coordination sequence of the diamond net is determined.     

Graphs whose vertices are graphs with bounded degree: Distance problems

By an f-graph we mean a graph having no vertex of degree greater than f. Let U(n,f) denote the graph whose vertex set is the set of unlabeled f-graphs of order n and such that the vertex corresponding to the graph G is adjacent to the vertex corresponding to the graph H if and only if H is obtainable from G by either the insertion or the deletion of a single edge. The distance between two graphs G and H of order n is defined as the least number of insertions and deletions of edges in G needed to obtain H. This is also the distance between two vertices in U(n,f). For simplicity, we also refer to the vertices in U(n,f) as the graphs in U(n,f). The graphs in U(n,f) are naturally grouped and ordered in levels by their number of edges. The distance nf/2 from the empty graph to an f-graph having a maximum number of edges is called the height of U(n,f). For f =2 and for f≥(n-1)/2, the diameter of U(n,f) is equal to the height. However, there are values of the parameters where the diameter exceeds the height. We present what is known about the following two problems: (1) What is the diameter of U(n,f) when 3≥f<(n-1)/2? (2) For fixed f, what is the least value of n such that the diameter of U(n,f) exceeds the height of U(n,f)?     

On walks in molecular graphs.

Walks in molecular graphs and their counts for a long time have found applications in theoretical chemistry. These are based on the fact that the (i, j)-entry of the kth power of the adjacency matrix is equal to the number of walks starting at vertex i, ending at vertex j, and having length k. In recent papers (refs 13, 18, 19) the numbers of all walks of length k, called molecular walk counts, mwc(k), and their sum from k = 1 to k = n - 1, called total walk count, twc, were proposed as quantities suitable for QSPR studies and capable of measuring the complexity of organic molecules. We now establish a few general properties of mwc's and twc among which are the linear dependence between the mwc's and linear correlations between the mwc's and twc, the spectral decomposition of mwc's, and various connections between the walk counts and the eigenvalues and eigenvectors of the molecular graph. We also characterize the graphs possessing minimal and maximal walk counts.     

Reaction route graphs. III. Non-minimal kinetic mechanisms

The concept of reaction route (RR) graphs introduced recently by us for kinetic mechanisms that produce minimal graphs is extended to the problem of non-minimal kinetic mechanisms for the case of a single overall reaction (OR). A RR graph is said to be minimal if all of the stoichiometric numbers in all direct RRs of the mechanism are equal to +/-1 and non-minimal if at least one stoichiometric number in a direct RR is non-unity, e.g., equal to +/-2. For a given mechanism, four unique topological characteristics of RR graphs are defined and enumerated, namely, direct full routes (FRs), empty routes (ERs), intermediate nodes (INs), and terminal nodes (TNs). These are further utilized to construct the RR graphs. One algorithm involves viewing each IN as a central node in a RR sub-graph. As a result, the construction and enumeration of RR graphs are reduced to the problem of balancing the peripheral nodes in the RR sub-graphs according to the list of FRs, ERs, INs, and TNs. An alternate method involves using an independent set of RRs to draw the RR graph while satisfying the INs and TNs. Three examples are presented to illustrate the application of non-minimal RR graph theory.     

Nonbonding orbitals in fullerenes: nuts and cores in singular polyhedral graphs

A zero eigenvalue in the spectrum of the adjacency matrix of the graph representing an unsaturated carbon framework indicates the presence of a nonbonding pi orbital (NBO). A graph with at least one zero in the spectrum is singular; nonzero entries in the corresponding zero-eigenvalue eigenvector(s) (kernel eigenvectors) identify the core vertices. A nut graph has a single zero in its adjacency spectrum with a corresponding eigenvector for which all vertices lie in the core. Balanced and uniform trivalent (cubic) nut graphs are defined in terms of (-2, +1, +1) patterns of eigenvector entries around all vertices. In balanced nut graphs all vertices have such a pattern up to a scale factor; uniform nut graphs are balanced with scale factor one for every vertex. Nut graphs are rare among small fullerenes (41 of the 10 190 782 fullerene isomers on up to 120 vertices) but common among the small trivalent polyhedra (62 043 of the 398 383 nonbipartite polyhedra on up to 24 vertices). Two constructions are described, one that is conjectured to yield an infinite series of uniform nut fullerenes, and another that is conjectured to yield an infinite series of cubic polyhedral nut graphs. All hypothetical nut fullerenes found so far have some pentagon adjacencies: it is proved that all uniform nut fullerenes must have such adjacencies and that the NBO is totally symmetric in all balanced nut fullerenes. A single electron placed in the NBO of a uniform nut fullerene gives a spin density distribution with the smallest possible (4:1) ratio between most and least populated sites for an NBO. It is observed that, in all nut-fullerene graphs found so far, occupation of the NBO would require the fullerene to carry at least 3 negative charges, whereas in most carbon cages based on small nut cubic polyhedra, the NBO would be the highest occupied molecular orbital (HOMO) for the uncharged system.     

Graph theory and the PPP method

A graph theoretical formulation of the PPP method is presented. A weighted adjacency matrix of the PPP graph is given, wherein the off-diagonal elements are the bond orders. The automorphism group of the PPP graph is defined and shown to be isomorphic with the permutational subgroup of the permutation-inversion group of the molecule. It is demonstrated that the characteristic polynomial of the adjacency matrix of the PPP bond graph is invariant in every SCF iteration. It is shown that the PPP spectra discriminate isospectral graphs.Camille and Henry Dreyfus Teacher-Scholar.     

On the ABC index of connected graphs with given degree sequences

The atom-bond connectivity (ABC) index of a graph G is defined to be \(ABC(G)=\sum _{uv\in E(G)}\sqrt{\frac{d(u)+d(v)-2}{d(u)d(v)}}\) where d(u) is the degree of a vertex u. The ABC index plays a key role in correlating the physical–chemical properties and the molecular structures of some families of compounds. In this paper, we describe the structural properties of graphs which have the minimum ABC index among all connected graphs with a given degree sequence. Moreover, these results are used to characterize the extremal graphs which have the minimum ABC index among all unicyclic and bicyclic graphs with a given degree sequence.     

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.     

Note on the topological information content of simple graphs

It is shown that simple graphs gave equal topological information content if their automorphism groups are isomorphic. Further, if the automorphism groups of two graphs are represented by wreath products of which the inner groups are isomorphic, then the two graphs possess equal topological information content. Three graphs which correspond to organic molecules illustrate this finding.Dedicated to Professor Dr.Karl Schlögl on the occasion of his 60th birthday.     

Common vertex matrix: A novel characterization of molecular graphs by counting

We present a novel matrix representation of graphs based on the count of equal‐distance common vertices to each pair of vertices in a graph. The element (i, j) of this matrix is defined as the number of vertices at the same distance from vertices (i, j). As illustrated on smaller alkanes, these novel matrices are very sensitive to molecular branching and the distribution of vertices in a graph. In particular, we show that ordered row sums of these novel matrices can facilitate solving graph isomorphism for acyclic graphs. This has been illustrated on all undecane isomers C₁₁H₂₄ having the same path counts (total of 25 molecules), on pair of graphs on 18 vertices having the same distance degree sequences (Slater's graphs), as well as two graphs on 21 vertices having identical several topological indices derived from information on distances between vertices. © 2013 Wiley Periodicals, Inc.     

On acyclic molecular graphs with maximal Hosoya index, energy, and short diameter

The total number of matchings of a graph is defined as its Hosoya index. Conjugated and non-conjugated acyclic graphs that have maximal Hosoya index and short diameter are characterized in this paper, explicit expressions of the Hosoya indices of these extremal graphs are also presented.     

Wiener indices of trees and monocyclic graphs with given bipartition

The Wiener index of a connected graph is defined as the sum of distances between all unordered pairs of its vertices. It has found various applications in chemical research. We determine the minimum and the maximum Wiener indices of trees with given bipartition and the minimum Wiener index of monocyclic graphs with given bipartition, respectively. We also characterize the graphs whose Wiener indices attain these values. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

The branching graphs of polyhexes: Some elementary theorems,conjectures and open questions

This paper presents a few novel results, and collects together what is known and conjectured about the branching graph of a polyhex.     

Minimal energy of unicyclic graphs of a given diameter

The energy of a graph is defined as the sum of the absolute values of all the eigenvalues of the graph. For a given positive integer d with , we characterize the graphs with minimal energy in the class of unicyclic graphs with n vertices and a given diameter d.