Kekuléan benzenoids

A Kekulé structure for a benzenoid or a fullerene $\Gamma $ is a set of edges $K$ such that each vertex of $\Gamma $ is incident with exactly one edge in $K$ , i.e. a perfect matching. All fullerenes admit a Kekulé structure; however, this is not true for benzenoids. In this paper, we develop methods for deciding whether or not a given benzenoid admits a Kekulé structure by constructing Kekulé structures that have a high density of benzene rings. The benzene rings of the Kekulé structure $K$ are the faces in $\Gamma $ that have exactly three edges in $K$ . The Fries number of $\Gamma $ is the maximum number of benzene rings over all possible Kekulé structures for $\Gamma $ and the set of benzene rings giving the Fries number is called a Fries set. The Clar number is the maximum number of independent benzene rings over all possible Kekulé structures for $\Gamma $ and the set of benzene rings giving the Clar number is called a Clar set. Our method of constructing Kekulé structures for benzenoids generally gives good estimates for the Clar and Fries numbers, often the exact values.     

Computing the Kekulé structure count for alternant hydrocarbons

A fast computer algorithm brings computation of the permanents of sparse matrices, specifically, molecular adjacency matrices. Examples and results are presented, along with a discussion of the relationship of the permanent to the Kekulé structure count. A simple method is presented for determining the Kekulé structure count of alternant hydrocarbons. For these hydrocarbons, the square of the Kekulé structure count is equal to the permanent of the adjacency matrix. In addition, for alternant structures the adjacency matrix for N atoms can be written in such a way that only an N/2 × N/2 matrix need be evaluated. The Kekulé structure count correlates with topological indices. The inclusion of the number of cycles improves the fit. When comparing with previous results, the variance decreases 74%. The calculated standard heat of formation correlates with the logarithm of the Kekulé structure count. This heat increments 349 kJ/mol each time the Kekulé structure count increases by one order of magnitude. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Innate degree of freedom of a graph

For a Kekulé structure we consider the smallest number of placements of double bonds such that the full Kekulé structure on the given parent graph is fully determined. These numbers for each Kekulé structure of the parent graph sum to a novel structural invariant F, called the degree of freedom of the graph. Some qualitative characteristics are identified, and it is noted that apparently it behaves differently from a couple of other invariants related to Kekulé structures.     

On the Anti-forcing Number of Benzenoids

The anti-forcing number is introduced as the smallest number of edges that have to be removed that any benzenoid remains with a single Kekulé structure. Similarly, the anti- Kekulé number is discussed as the smallest number of edges that have to be removed that any benzenoid remains connected but without any Kekulé structure. These concepts have been exemplified on damaged benzenoid parallelograms.     

π‐electron currents in polycyclic conjugated hydrocarbons: Coronene and its isomers having five and seven member rings

We have outlined novel graph theoretical model for computing π‐electron currents in π‐electron polycyclic conjugated hydrocarbons. We start with Kekulé valence structures of a polycyclic conjugated hydrocarbon and their conjugated circuits. To each 4n+2 conjugated circuits we assign counter clockwise current i and to each 4n conjugated circuit we assign clockwise current i. By adding the contributions from all conjugated circuits in a single Kekulé valence structure one obtains π‐electron current pattern for the particular Kekulé valence structure. By adding the conjugated circuit currents in all Kekulé valence structure one obtains the pattern of π‐electron currents for considered molecule. We report here π‐electron current patters for coronene and 17 its isomers, which have been recently considered by Balaban et al., obtained by replacing one or more pairs of peripheral benzene rings with five and seven member rings. Our results are compared with their reported π‐electron current density patters computed by ab initio molecular orbital (MO) computations and satisfactory parallelism is found between two so disparate approaches. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Kekulé’s Oscillating D3h Cyclohexatriene Structure of Benzene

Kekulé postulated that neighbouring carbon atoms in benzene undergo incessant collision with each other, thereby leading to the interchange of double and single bonds, which amounts to an oscillation between two cyclohexatriene structures in dynamic equilibrium. It has been claimed that Kekulé arrived at a fully symmetric D_6h structure of benzene and that the oscillation hypothesis should not be attributed to him. However, Clausius’ collision theory, which was known at the time, implies that, when the absolute temperature approaches zero, the collision frequency will tend toward zero too, i.e. collisions will stop, and a static, D_3h cyclohexatriene obtains. The classical collision theory did not allow Kekulé to construct the desired D_6h structure as the energy minimum. The theory of harmonic oscillators would have allowed it, but that was not attempted at Kekulé’s time.     

Clar chains and a counterexample

A fullerene is a 3-regular plane graph with only pentagonal and hexagonal faces. The Fries and Clar number of a fullerene are two related parameters, and the Clar number is less understood. We introduce the Clar Structure of a fullerene, a decomposition designed to compute the Clar number for classes of fullerenes. We also settle an open question with a counterexample: we prove that the Clar and Fries number of a fullerene cannot always be obtained with the same Kekulé structure.     

Counterexamples to a proposed algorithm for Fries structures of benzenoids

The Fries number of a benzenoid is the maximum number of benzenoid hexagons over all of its Kekulé structures (perfect matchings), and a Fries canonical structure is a perfect matching that realises this maximum. A recently published algorithm claims to determine Fries canonical structures of benzenoids via iterated Hadamard products based on the adjacency matrix (Ciesielski et?al. in Symmetry 2:1390–1400, 2010). This algorithm is re-examined here. Convergence is typically rapid and often yields a single candidate perfect matching, but the algorithm can give an exponential number of choices, of which only a small number are canonical. More worryingly, the algorithm is found to give incorrect results for the Fries number for some benzenoids with as few as seven hexagonal faces. We give a combinatorial reformulation of the algorithm in terms of linear combinations of perfect matchings (with weights at each stage proportional to the products of weights of the edges included in a matching). In all the cases we have examined, the algorithm converges to a maximum-weight matching (or combination of maximum-weight matchings), and where the algorithm fails, either no best Fries matching is of maximum weight, or a best Fries matching is of maximum weight but a sub-optimal matching of the same weight is chosen.     

Relating Total π-Electron Energy and Resonance Energy of Benzenoid Molecules with Kekulé- and Clar-Structure-Based Parameters

Summary. Within classes of isomeric benzenoid hydrocarbons various Kekulé- and Clar-structure-based parameters (Kekulé structure count, Clar cover count, Herndon number, Zhang–Zhang polynomial) are all mutually correlated. This explains why both the total π-electron energy (E), the Dewar resonance energy (DRE), and the topological resonance energy (TRE) are well correlated with all these parameters. Nevertheless, there exists an optimal value of the variable of the Zhang–Zhang polynomial for which it yields the best results. This optimal value is negative-valued for E, around zero for TRE, and positive-valued for DRE. A somewhat surprising result is that TRE and DRE considerably differ in their dependence on Kekulé- and Clar-structure-based parameters.     

Ordering of Kekulé structures using nonadjacent numbers

Kekulé indices and conjugated circuits are computed for 36 Kekulé structures, together with two VB quantities associated with the corresponding factor graphs (previously called submolecules). These latter quantitites are nonadjacent numbers of Hosoya and the reciprocal of the connectivity indices of Randi?. It was found that the index of Hosoya successfully orders a set of Kekulé structures belonging to the same hydrocarbon in a parallel order as their Kekulé indices and branching indices. This substantiates the relation between VB and MO theories. A code is derived by summing contributions of nonadjacent numbers in all Kekulé stuctures of a hydrocarbon. The order of the resulting codes is found to be identical to the order of the molecular properties (resonance energies, π-energies, and eigenvalues) of the hydrocarbons.     

Relating Total π-Electron Energy and Resonance Energy of Benzenoid Molecules with Kekulé- and Clar-Structure-Based Parameters

Within classes of isomeric benzenoid hydrocarbons various Kekulé- and Clar-structure-based parameters (Kekulé structure count, Clar cover count, Herndon number, Zhang–Zhang polynomial) are all mutually correlated. This explains why both the total π-electron energy (E), the Dewar resonance energy (DRE), and the topological resonance energy (TRE) are well correlated with all these parameters. Nevertheless, there exists an optimal value of the variable of the Zhang–Zhang polynomial for which it yields the best results. This optimal value is negative-valued for E, around zero for TRE, and positive-valued for DRE. A somewhat surprising result is that TRE and DRE considerably differ in their dependence on Kekulé- and Clar-structure-based parameters.     

Coding and ordering Kekulé structures

The concept of numerical Kekulé structures is used for coding and ordering geometrical (standard) Kekulé structures of several classes of polycyclic conjugated molecules: catacondensed, pericondensed, and fully arenoid benzenoid hydrocarbons, thioarenoids, and [N]phenylenes. It is pointed out that the numerical Kekulé structures can be obtained for any class of polycyclic conjugated systems that possesses standard Kekulé structures. The reconstruction of standard Kekulé structures from the numerical ones is straightforward for catacondensed systems, but this is not so for pericondensed benzenoid hydrocarbons. In this latter case, one needs to use two codes to recover the geometrical Kekulé structures: the Wiswesser code for the benzenoid and the numerical code for its Kekulé structure. There is an additional problem with pericondensed benzenoid hydrocarbons; there appear numerical Kekulé structures that correspond to two (or more) geometrical Kekulé structures. However, this problem can also be resolved.     

Algebraic Kekulé formulas for benzenoid hydrocarbons

By assigning two pi-electrons of CC double bonds in a Kekulé valence structure to a benzene ring if not shared by adjacent rings and one pi-electron if CC double bond is shared by two rings we arrived at numerical valence formulas for benzenoid hydrocarbons. We refer to numerical Kekulé formulas as algebraic Kekulé valence formulas to contrast them to the traditional geometrical Kekulé valences formulas. The average over all numerical Kekulé valence structures results in a single numerical structure when a benzenoid hydrocarbon molecule is considered. By ignoring numerical values the novel quantitative formula transforms into a qualitative one which can replace incorrectly used notation of pi-electron sextets to indicate aromatic benzenoids by placing inscribed circles in adjacent rings-which contradicts Clar's characterization of benzenoid hydrocarbons.     

Algebraic Structure Count of Some Cyclic Hexagonal-Square Chains on the Möbius Strip

The concept of ASC (Algebraic structure count) is introduced into theoretical organic chemistry by Wilcox as the difference between the number of so-called “even” and “odd” Kekulé structures of a conjugated molecule. Precisely, algebraic structure count (ASC-value) of the bipartite graph G corresponding to the skeleton of a conjugated hydrocarbon is defined by where A is the adjacency matrix of G. The determination of algebraic structure count of (bipartite) cyclic hexagonal-square chains in the the class of plane such graphs is known. In this paper we expand these considerations on the non-plane class. An explicit combinatorial formula for ASC is deduced in the special case when all hexagonal fragments are isomorphic.     

A combination of Clar number and Kekulé count as an indicator of relative stability of fullerene isomers of C<Subscript>60</Subscript>

Kekulé count is not as useful in predicting the thermodynamic stability of fullerenes as it is for benzenoid hydrocarbons. For example, the Kekulé count of the icosahedral C₆₀, the most stable fullerene molecule, is surpassed by its 20 fullerene isomers (Austin et al. in Chem Phys Lett 228:478–484, 1994). This article investigates the role of Clar number in predicting the stability of fullerenes from Clar’s ideas in benzenoids. We find that the experimentally characterized fullerenes attain the maximum Clar numbers among their fullerene isomers. Our computations show that among the 18 fullerene isomers of C₆₀ achieving the maximum Clar number (8), the icosahedral C₆₀ has the largest Kekulé count. Hence, for fullerene isomers of C₆₀, a combination of Clar number and Kekulé count predicts the most stable isomer.     

Ground-state properties of benzenoid hydrocarbons by simple bond orbital resonance theory approach

π-electron energies and bond orders of benzenoid hydrocarbons with up to five fused hexagons have been considered by the simple Bond Orbital Resonance Theory (BORT) approach. The corresponding ground states were determined according to four BORT models. In the first three models a diagonalisation of the Hückel-type Hamiltonian was performed in the bases of Kekulé, of Kekulé and mono-Claus and of Kekulé and Claus resonance structures, respectively. In the fourth model a simple BORT ansatz was used. According to this ansatz, the ground state is a linear combination of the positive Kekulé structures, all with equal coefficients. It was shown that π-electron energies and bond orders obtained by these models correlate much better with the PPP energies and bond orders than with the Hückel energies and bond orders. This indicates that a simple BORT approach is quite reliable in predicting the more sophisticated PPP results. Concerning the relative performance of the four BORT models, the best results were obtained with the BORT ansatz. The performance deteriorates with the expansion of the basis set. This is attributed to the fact that in these models the improvement of the basis set is not accompanied with the corresponding improvement of the Hamiltonian. Comparing the BORT-ansatz bond orders with the Pauling bond orders, it was shown that BORT-ansatz bond orders correlate much better with the PPP bond orders. This revised version was published online in July 2006 with corrections to the Cover Date.     

The Mesomeric Effect of Thiazolium on non‐Kekulé Diradicals in Pichia stipitis Transketolase

It is theoretically plausible that thiazolium mesomerizes to congeners other than carbene in a low effective dielectric binding site; especially given the energetics and uneven electronegativity of carbene groups. However, such a phenomenon has never been reported. Nine crystal structures of transketolase obtained from Pichia stipitis (TKps) are reported with subatomic resolution, where thiazolium displays an extraordinary ring‐bending effect. The bent thiazolium congeners correlate with non‐Kekulé diradicals because there is no gain or loss of electrons. In conjunction with biophysical and biochemical analyses, it is concluded that ring bending is a result of tautomerization of thiazolium with its non‐ Kekulé diradicals, exclusively in the binding site of TKps. The chemophysical properties of these thiazolium mesomers may account for the great variety of reactivities carried out by thiamine–diphosphate‐containing (ThDP) enzymes. The stability of ThDP in living systems can be regulated by the levels of substrates, and hydration and dehydration, as well as diradical‐mediated oxidative degradation.     

Heats of atomization of some conjugated molecules containing nitrogen or oxygen by a novel semiempirical method

Heats of atomization for a range of conjugated molecules containing nitrogen or oxygen are calculated by a semiempirical method that combines some features of both the MO and VB theories. The π ground state of each conjugated molecule is represented as a linear combination of Kekulé structures. Unlike in the VB theory, each Kekulé structure is a determinant containing bond orbitals. Here experimental heats of atomization are reproduced approximately as well as by the more sophisticated SCF –MO approach. The use of this method is, however, much simpler since it amounts to a single diagonalization of a matrix of the order equal to the number of Kekulé structures only.     

The number of Kekulé structures of polyominos on the torus

Let G be a (molecule) graph. A perfect matching, or Kekulé structure of G is a set of independent edges covering every vertex exactly once. Enumeration of Kekulé structures of a (molecule) graph is interest in chemistry, physics and mathematics. In this paper, we focus on some polyominos on the torus and obtain the explicit expressions on the number of the Kekulé structures of them.