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Quality testing of spectrum-based distance descriptors for polycyclic aromatic hydrocarbons with applications to carbon nanotubes and nanocones
⁎Corresponding authors. sakander.hayat@giki.edu.pk (Sakander Hayat), m.imran658@uaeu.ac.ae (Muhammad Imran)
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Received: ,
Accepted: ,
This article was originally published by Elsevier and was migrated to Scientific Scholar after the change of Publisher.
Abstract
In this paper, we investigate the predictive potential of commonly occurring spectrum-based distance descriptors which are based on eigenvalues of distance-related chemical matrices. For our comparative testing, the normal boiling point has been chosen to be representative of van-der-Waals and intermolecular type interactions, whereas, the standard enthalpy/heat of formation is selected to represent thermal properties. We introduce three new chemical matrices and results show that the spectral descriptors based on these new matrices outperform the existing well-studied spectral descriptors. A computational method is used to calculate commonly occurring spectrum-based distance descriptors to investigate their correlation ability with the experimental data for the two chosen physicochemical properties for lower polycyclic aromatic hydrocarbons. By providing the list of the five best spectrum-based distance descriptors, our study contributes towards putting forward the best spectrum-based topological descriptors while mentioning the ones which do not deserve further attention of researchers. Applications of our results to certain families of carbon polyhex nanotubes and one-hexagonal nanocones have been presented. The results can potentially be used to determine certain physicochemical of these nanotubes and nanocones theoretically with higher accuracy and negligible error.
Keywords
Mathematical chemistry
Chemical graph theory
Graphical indices
QSAR/QSPR models
Carbon nanostructures
05C92
05C09
05C90

1 Introduction
1.1 Research background
Quantitative structure activity/property relationship (QSAR/QSPR) methods provide efficient correlation of physicochemical characteristics and the bioactivities of chemical compounds. Structure-based topological indices/descriptors assist in generating efficient regression models for these properties with strong prediction power. The pioneer work on graph-theoretic structure-based topological descriptors was started in 1947 by Wiener (1947) who proposed the path number of a graph defined as the distances sum between all ordered pairs of vertices of graphs. The structurally-invariant path number, which later was renamed as the Wiener index, was found to correlate well with the boiling point of alkanes. The Wiener index was the first structurally-invariant topological descriptor.
Generally speaking, the transformation of a molecular graph into a mathematical real number is performed by these topologically-invariant quantities called topological/structure index/descriptor, where a molecular/chemical graph is a hydrogen-depleted molecular structure in which edges correspond to bonds, whereas, vertices correspond to atoms in the underlying chemical compound. The study of these chemical graphs is known as the chemical graph theory. Physicochemical characteristics such as the normal boiling point, the enthalpy of vaporization, the standard heat/enthalpy of formation, the critical pressure, the critical volume, the critical temperature etc. are subsequently correlated by these structurally- and topologically-invariant graph-theoretic descriptors which provide regression models for these characteristics with strong correlation powers. Quantum-theoretic properties such as the total -electron energy have also been correlated by spectrum-based descriptors. For instance, predictive potential of certain classes of topological descriptors to correlate the -electronic energy have been studied in Hayat et al. (2020a,c, 2019a).
Well-known classes of topological descriptors include distance-based descriptors (Xu et al., 2014), valency/degree-based descriptors (Gutman, 2013), eigenvalues-based topological descriptors (Consonni and Todeschini, 2008), and counting related topological polynomials and descriptors (Hosoya, 1988). Spectrum-based topological descriptors induce regression models with significantly more efficiency for various physical and chemical properties such as the boiling point and the enthalpy of formation. They are defined based on eigenvalues of certain distance-related or valency-related chemical matrices. Hundreds of molecular descriptors (Gutman and Furtula, 2010; Todeschini and Consonni, 2009) have been proposed so far. The absence of any rigorous criterion to slowdown their number makes the number of proposed molecular descriptors increasing constantly. A considerably big portion of these molecular descriptors are graph-theoretic topological structure descriptors. Consequently, without having any firm criterion to put forward the descriptors which deserve further attention and meanwhile mentioning the ones which show poor performance, there are far too many structure descriptors than there should be.
To put forward the best topological descriptors while mentioning the ones which do not deserve further attention of researchers, Gutman and Tošović (2013) conducted a comparative testing for isomeric octanes. Hayat et al. (2020b) conducted a similar comparative testing for lower benzenoid hydrocarbons for the class of distance-based topological descriptors. Recently, Hayat and Khan (2021) extended the same comparative testing to the class of spectrum-based valency descriptors, which in turn, provides a basic motivation to study the class of spectrum-based distance descriptors. In this paper, we consider the class of graph-theoretic descriptors which are defined based on eigenvalues of distance-related chemical matrices.
Main contributions of this paper are as follows:
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A computational technique for computing spectrum-based distance descriptors has been proposed. Comparative analyses with related computational techniques show that our method has less computational complexity and is more diverse in computing spectral descriptors.
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Three new chemical matrices have been proposed and their spectral descriptors show potential in chemical applications.
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The proposed computational method is used to investigate correlation of spectrum-based topological descriptors with the normal boiling point and standard enthalpy of formation for benzenoid hydrocarbons to test their quality.
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Some favorable and some unexpected outcomes have been reported based on the quality testing.
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The newly proposed second ABC Estrada index showcase the best performance among all spectrum-based distance descriptors.
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Applications to certain infinite families of carbon nanotubes and nanocones have been reported.
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Our results help in correlating certain physicochemical properties of these nanostructures.
1.2 literature review
This subsection provides a detailed literature review available on spectrum-based distance descriptors defined in Section 2.
Indulal (2009) and Zhou and Ilić (2010) studied extremal graphs with respect to the distance spectral radius. Indulal et al. (2008), Indulal (2009) and Zhou and Ilić (2010) derived some sharp upper and lower bounds on the distance energy and characterized corresponding extremal graphs. Moreover, Bozkurt et al. (2010) studied distance equi-energetic graphs. Güngör and Bozkurt (2009) introduced and studied the distance Estrada index of graphs. Shang (2020) devised a way to estimate the distance Estrada index of graphs. We also suggest a detailed survey on the distance spectrum of graphs by Aouchiche and Hansen (2014).
The distance Laplacian matrix was introduced by Aouchiche and Hansen (2013) and derived some extremal results on the distance Laplacian spectral radius of graphs. Das et al. (2018) defined the distance Laplacian energy of graphs and derived a relationship between the distance energy and distance Laplacian energy of graphs. Shang (2015) studied the Laplacian Estrada index for evolving graphs.
Aouchiche and Hansen (2016) & Medina et al. (2020) showed some extremal results on the distance signless Laplacian spectral radius and characterized the graphs achieving those bounds. Alhevaz et al. (2018), Medina et al. (2020) and Alhevaz et al. (2021) derived certain extremal results on the distance signless Laplacian energy of graphs. Alhevaz et al. (2021, 2019) derived some sharp upper and lower bounds on the distance signless Laplacian Estrada index of graphs.
Cui and Liu (2012) studied Harary eigenvalues and found some upper and lower bounds on the Harary energy and Estrada index of graphs. Jahanbani (2019) found some new bounds on the Harary energy and Estrada index of graphs. Fath-Tabar et al. (2010) studied the Szeged eigenvalues and related spectral descriptors of graphs. Najdafi-Arani (2011) showed some sharp bounds on the PI energy of graphs. Corresponding extremal graphs were also characterized in Najdafi-Arani (2011).
Kanna et al. (2019) showed some sharp upper and lower bounds on the degree-distance energy of graphs. The Schultz matrix (Schultz, 1989) was shown to possess potential applications in predicting the normal boiling points of alkanes. Roshan and Sarasija (2019) defined the Gutman covering matrix of graphs. They derived some sharp upper and lower bounds on the Gutman covering energy of graphs.
2 Spectrum-based distance descriptors
Mathematically, a graph is nothing but an order pair comprising a set of points called vertices and connection between those pairs of points called edges. A chemical/molecular graph is a hydrogen-depleted chemical structure obtained from a chemical compound. Vertices (resp. edges) in a chemical graph correspond to atoms (resp. bonds) in the underlying chemical compound. Two vertices are called adjacent if there is an edge between. The number of adjacent vertices to a given vertices is called the degree or valency of x and is denoted by . A vertex degree in a chemical graph, corresponding to an organic chemical compound, can be at most four, since the valency of the carbon atom is four. For more notations and terminologies on chemical graph theory, we refer the reader to Diudea et al. (2001) and Gutman and Polansky (1986).
Topological descriptors are mathematical functions mapping simple connected graphs to real numbers having significant applications in chemistry (Balaban et al., 1983). Valency/degree-based topological descriptors possess defining structures based on valencies of vertices, whereas, the defining structures of distance-based topological descriptors are based on distances between vertices in graphs. The atom-bond connectivity index, the Randić connectivity index, the sum-connectivity index and Zagreb indices, among others, are examples of valency-based descriptors. The Wiener index, the Balaban index, the Szeged index, among others, are included in the examples of distance-based descriptors. Spectrum-based topological descriptors comprise the defining structure based on eigenvalues of distance-related or valency-related chemical matrices. The adjacency energy, the Estrada index, the distance energy and Estrada index and Laplacian & signless Laplacian energies and Estrada indices, among many others, are included in the list of spectrum-based topological descriptors. Hosamani et al. (2017) reviewed various results on energies of different graph-related matrices. For a book on adjacency energy, we refer to Li et al. (2012). Moreover, for a book on the spectral radius of different graphical matrices, we refer to Stevanović (2014). Certain computational results on degree and distance-based topological descriptors are presented in Hayat (2017), Hayat and Imran (2014), Hayat et al. (2019b), and Hayat et al. (2020b).
Next we define some well-known distance-related chemical matrices. Later, spectrum-based distance descriptors are defined based on the eigenvalues of these matrices.
2.1 Existing distance-based chemical matrices
We start with the well-known classical distance matrix of graphs.
2.1.1 The distance matrix
Although, concept of the distance matrix goes back to Cayley (1841) who used it in a geometric setting. Its graph-theoretic spectral study begin formally in 20th century, see for instance (Young and Householder, 1938). In 1971, Graham and Pollack (1971) established a relationship between the number of negative eigenvalues of the distance matrix and the addressing problem in data communication systems.
The distance matrix of an n-vertex graph is an symmetric matrix defined as where is the distance between vertices u and v in .
2.1.2 The distance Laplacians
Let be an n-vertex graph. The transmission of a vertex is defined to be the sum of distances between all vertices of and the fixed vertex u. The average transmission of a graph is defined as follows: The total transmission of a graph is defined to be the sum of distances between all unordered pairs of vertices in . Clearly, The transmission vector of is an vector denoted by and defined as for all . Let be the diagonal matrix corresponding the vector such that . The distance Laplacian matrix is an symmetric matrix defined as Similarly, the distance signless Laplacian matrix of an n-vertex graph is an symmetric matrix defined as where is the distance matrix of .
2.1.3 The Harary matrix
The Harary matrix has recently been introduced by Güngör and Çevik (2010). For an n-vertex graph , the Harary matrix is an symmetric matrix defined as
2.1.4 The Szeged matrix
Before defining the Szeged matrix of a graph, we need some necessary definitions. Corresponding to an edge of a graph , we define the following parameters:
Based on the quantities and , Diudea et al. (1997) introduced the Szeged matrix of graphs. For an n-vertex graph , the Szeged matrix is an symmetric matrix defined as
2.1.5 The Padmakar-Ivan (PI) matrix
The Padmakar-Ivan (PI) matrix and related spectrum-based descriptors were introduced by Najdafi-Arani (2011). The PI matrix of an n-vertex graph is an symmetric matrix defined as
2.1.6 The degree-distance matrix
The degree-distance matrix was introduced by Dobrynin and Kochetova (1994) in term of the degree-distance index of graphs. The degree-distance matrix of an n-vertex graph is an symmetric matrix defined as
2.1.7 The Schultz matrix
Let be the adjacency matrix of and be the distance matrix of . Introduced by Schultz (1989) in 1989, the Schultz matrix is defined as follows:
2.2 Some new chemical matrices
In this subsection, we define some new chemical matrices and investigate chemical applicability of corresponding spectrum-based distance descriptors in QSAR studies. Note that these matrices correspond to some well-established distance-based topological descriptors of graphs.
2.2.1 The second atom-bond connectivity matrix
The general atom-bond connectivity index of a graph is defined as follows: For , we have ( )=( ), where is the degree/valency of u in . The first ABC index was proposed by Estrada et al. (1998). Graovac and Ghorbani (2010) considered ( )=( ) and named it the second version of the ABC index.
Since most of the chemical matrices are actually based on some corresponding topological descriptors, we introduce a chemical matrix based on the second atom-bond connectivity index. Therefore, the second atom-bond connectivity matrix of an n-vertex graph is an symmetric matrix defined as
2.2.2 The second geometric-arithmetic matrix
The general geometric-arithmetic (GA) index of a graph is defined as follows: If ( )=( ), then . The index was proposed by Vukičević and Furtula (2009). Fath-Tabar et al. (2010) by considering ( )=( ), introduced the second version of the GA index.
Based on the second geometric-arithmetic index of an n-vertex graph , the second geometric-arithmetic matrix is an symmetric matrix defined as
2.2.3 The Gutman matrix
The Gutman index was introduced by Gutman (1994) in 1994 as a multiplicative version of the so-called degree-distance index. It is defined as
Based on the defining structure of the Gutman index, we define the Gutman matrix of an n-vertex graph to be an symmetric matrix defined as follows:
2.3 Spectrum-based distance descriptors
A spectrum-based descriptor defined based on the eigenvalues of a distance-related chemical matrix is said to be a spectrum-based distance descriptor.
For an n-vertex graph , let be a chemical matrix of defined in the previous subsection. Let be the eigenvalues of M. In this paper, we consider the following spectral descriptors corresponding to a chemical matrix M.
The M spectral radius is simply defined to be the largest eigenvalues of M: The energy of M, sometimes called M-energy, is defined as follows: The Estrada index of M, also called M-Estrada index, is defined as follows:
For distance Laplacians, the spectral descriptors are defined differently. If and be its eigenvalues. Then spectral radius is defined similarly as for the matrix M. The distance Laplacian or signless Laplacian energy is defined as follows: The distance Laplacian or signless Laplacian Estrada index is defined as follows: The average transmission and the total transmission of a graph are defined in SubsubSection 2.1.2.
3 A unified computational method
In this section, we present a unified computational technique to compute all the spectrum-based topological descriptors in Section 2. The proposed technique is the main tool in computing these eigenvalues related topological descriptors for polycyclic aromatic compounds, carbon nanotubes and carbon nanocones in Sections 4, 5 & 6 respectively.
Among the other classes of topological descriptors such as valency-based descriptors, distance-based descriptors, counting related molecular descriptors, the class of eigenvalues-based topological descriptors is highly non-trivial and somewhat complicated since they are defined based on eigenvalues of graphical matrices. The branch of graph theory which derives certain structural properties of graphs from the eigenvalues of their related graph-theoretic matrices is called the spectral graph theory. Spectral graph theory assists in computing the eigenvalues of graphs on small order, say up to six vertices. There are also characterization results in spectral graph theory such as graphs with smallest eigenvalue at least studied in Desai and Rao (1994). For more details on spectral graph theory, we refer the reader to the book by Cvetković et al. (1995) and by Brouwer and Haemers (2012). Although there is a rich literature available on graph spectra but current tools do not assist in computing all the eigenvalues of higher-order graphs. Thus, it is essential to develop computational methods based on computer softwares to compute the complete spectrum of eigenvalues of a given matrix which corresponds to a graph with many vertices.
Before we go into the details of our proposed method, we review all known methods available in the literature. Ashrafi (2010, 2009) proposed a computer-based computational technique to calculate the adjacency energy and adjacency Estrada index of a chemical graph i.e. graph based on organic chemical structures and therefore have maximum valency up to 4. Their computational method makes use of certain computer software packages such as HyperChem (2002) to draw a chemical graph, Diudea et al. (2002) to calculate its adjacency matrix and finally GAP (The GAP Team, 1992) to calculate the adjacency energy and adjacency Estrada index. Hayat (2017) proposed a computational technique for various distance-based topological descriptors just by using newGraph (Stevanović et al.) and MatLab (MATLAB). Furthermore, a comparative analysis in Hayat (2017) with Ashrafi (2010) and Ashrafi and Sadati (2009) was also conducted to show that the former possesses less computational complexity and is more diverse in computing distance-based topological descriptors. Hayat et al. (2019b) extended the method in Hayat (2017) to the class of degree-distance-based and degree-based descriptors. Hayat et al. (2019a) presented a similar technique to compute the adjacency energy, the adjacency Estrada index and the inertia indices. In this paper, we extend the technique of Hayat et al. (2019a) to the 33 spectrum-based topological descriptors in Section 2.”In what follows, the method by Ashrafi (2010, 2009) is explained, for a chemical graph H, in a three-step algorithm:
Step 1: Draw H on HyperChem to obtain.hin file corresponding to H.
Step 2: Input the.hin file to Topocluj and calculate its adjacency matrix A. Topocluj will output the respective.m file.
Step 3: Insert the.m file in a GAP program developed by Ashrafi (2010) and Ashrafi and Sadati (2009) to calculate the A-energy and A-Estrada index of H.”.
Fig. 1 presents a flowchart of the method by Ashrafi et al.Flowchart of the technique by Ashrafi et al.
Although this method by Ashrafi et al. provides a platform to perform computational eigenvalue analysis for chemical graphs, it has certain disadvantages. For instance, it is restricted to chemical graphs which makes it not applicable for inorganic structures. Moreover, it is restricted to calculate the A-energy and A-Estrada index. We fill these gaps by proposing a unified computational method which can compute any spectrum-based descriptor from Section 2 while possesses less computational & algorithmic complexities. Rather than using HyperChem and Topolocluj for drawing a chemical graph and calculate its adjacency matrix, we use a single and more efficient platform i.e. newGraph (Stevanović et al.) which ”is a fully integrated environment used for improving a research process in graph theory. It is compatible both with conveniently drawing a general graph and then computing various graph-theoretic parameters including the adjacency and distance matrices. For a general graph G, our two-step computational method is explained as follows:”.
Step 1: ”Use newGraph as single platform to both draw G and calculate its distance matrix A.
Step 2: Insert the matrix A into our MatLab (MATLAB) program and compute any of the spectrum-based descriptor from Section 2.”.
Fig. 2 depicts a flowchart of our proposed method.Flowchart of our proposed method.
We have created a public open repository on GitHub where we have uploaded an early view of ReadMe file, our MatLab code and a PDF file to explain the work- ing pattern of our technique with a minimal working example (MWE). The GutHub page is accessible via https://github.com/Sakander/Distance-based-spectral-descriptors.git.
A comparative analysis has been conducted to measure the efficiency of our method with the method by Ashrafi et al. We fix two benzenoid hydrocarbons i.e. coronene and ovalene (see Fig. 3) for our comparative analysis. Computational complexity has been investigated for these two graphs and the data is provided in Table 1.The graphs of coronene and ovalene.
We also conduct comparative analysis between newGraph and Topolocluj & HyperChem in our method and Ashrafi and coauthors, respectively. Table 2 gives a detailed comparison between these two software packages and exhibits their pros and cons. Collectively Tables 1 & 2 provide a detailed comparative analysis between our method and the technique by Ashrafi et al. These tables shows that our proposed computational method is less computationally & algorithmically complex and more diverse in calculating spectrum-based topological descriptors.
Matlab
GAP
Input
Adjacency matrix
Adjacency matrix
Output
33 spectrum-based indices from Section 2
Energy and Estrada index
Computational time for coronene
0.021 s
1.325 s
Computational time for ovalene
0.023 s
1.624 s
newGraph
HyperChem
Valency/degree restriction
No restriction
At most 4
Efficiency in drawing
Significantly efficient
Good efficiency for chemical graphs
Matrix formatting
No formatting is required
Topocluj: Extensive matrix formatting
Availability to user
Freely available
Requires a user license
Space on disk
Pre-installation of Java with size 55 MB
264 MB
Invariants
newGraph: 91 graph invariants
Topocluj: 12 graph invariants
4 Predictive potential of spectrum-based distance descriptors
To investigate the correlation power and to determine the efficiency in quantitative structure activity/property relationship studies of spectrum-based topological descriptors, this section conducts a comparative testing to do the needful.
Standard enthalpy/heat of formation and normal boiling point are the standard chemical & physical properties which are opted for any comparative testing of topological descriptors. Chemically speaking, the normal boiling point is selected to advocate the van-der-Waals and intermolecular type interactions, whereas, the heat of formation is selected to be the representative of thermal characteristics. These two physicochemical characteristics are then correlated with a chosen set of topological descriptors. Better the correlation, better the prediction potential of a descriptors, is the simple criterion to access the performance of a topological descriptor.
Although it is customary to choose isomeric alkanes to be considered as molecules for this sort of comparative testings, we have selected lower polycyclic aromatic hydrocarbons (PAHs). The reason is that isomeric alkanes are thought to represent acyclic molecular structures, however, PAHs are considered to represent both cyclic and acyclic chemical structures. Graph-theoretic reasoning behind this fact is that trees are considered subgraphs of general graphs having cycles. Another reason of choosing PAHs is that some spectrum-based topological descriptors are defined to generalize the previously defined descriptors from acyclic structures to cyclic. Note further that for a comparative testing the number of molecules must be sufficiently large enough to acquire reliable and authentic statistical inferences. Moreover, the experimental data should be publicly available conveniently. Our choice of 22 lower polycyclic aromatic hydrocarbons meet both of these standard requirements. Fig. 4 exhibit the 22 PAHs with their aromaticity considered in this paper.”For experimental data regarding the normal boiling points of 22 lower polycyclic aromatic hydrocarbons (PAHs), we consulted the standard NIST databases (NIST Standard Reference Database) to acquire it. Moreover, the seminal work by Allison and Burgess (2015) provides the experimental data for the heat/enthalpy of formation for these polycyclic aromatic hydrocarbons. The acquired experimental data has been confirmed by tallying with a similar data available in the paper by Nikolić et al. (1998). We also refer the reader to a work by Putz et al. (2013, 2015) for an interesting interaction between topological descriptors, QSAR studies and PAHs.”The 22 polycyclic aromatic compounds (PAHs) considered for our comparative testing.
We use our proposed computational technique from Section 3 to calculate all the distance-based spectral descriptors from Section 2 for the 22 lower polycyclic aromatic hydrocarbons given in Fig. 4. Afterwards, the correlation is established between a topological descriptor and the experimental data for the normal boiling point and enthalpy of formation for the 22 PAHs. Although it is always preferably tried to establish a curvilinear correlation, we could not develop a curvilinear correlation for any of the spectrum-based distance descriptor. Thus, we measure the prediction power of a topological descriptor by evaluating its correlation coefficients with the physicochemical properties.”The data for such correlation coefficients with the normal boiling point as well as with the standard enthalpy/heat of formation for lower benzenoid hydrocarbons is provided in Table 3, in which
(resp. b.p.) denotes the standard heat of formation (resp. the normal boiling point) of a molecular structure.”.”It is important to notice in Table 3 that, for a given spectrum-based distance descriptor, the two correlation coefficients with the standard enthalpy of formation and the normal boiling point are considerably close to each other. This ensures us the significant appropriateness of our chosen physicochemical properties, very distinctive in nature though. This also suggests that these two physicochemical characteristics could be chosen to investigate the efficiency of any topological or molecular descriptor, in general.”
Topological index
4.1 Analysis of results
We have measured the efficiency of a topological descriptor in Table 3 by investigating the average of the two correlation coefficients. The simple criterion is that closer the average correlation coefficient to one, better the performance of topological descriptor is. Based on the average correlation coefficient, we have composed a list of top five best performing spectral descriptors. Table 4 gives the priority list for the five best spectrum-based distance descriptors. Table 5 provides a detailed statistical analysis for the prioritized five spectrum-based descriptors.
Topological descriptor
Position on the priority list
1
2
3
4
5
S.No
Index
Regression model
Statistics
1
2
3
4
5
Results support our newly defined spectrum-based distance descriptors as the second atom-bond connectivity Estrada index gives the best performance of them all. Moreover, two more newly introduced spectral descriptors based on the second geometric-arithmetic matrix make it to the top-five priority list. Those are the second geometric-arithmetic energy and Estrada index of graphs. Among the spectral descriptors available in the literature, the Harary energy and the degree-distance energy also make it to the”priority list of the five best spectrum-based distance descriptors. The results warrant further usage of the second atom-bond connectivity energy and Harary energy in the structure–activity and structure–property models.”.
The data in Table 3 suggests a number of favorable and unfavorable conclusions. By favorable outcome, we mean some less-known spectrum-based distance descriptors such as the Harary energy and the degree-distance energy etc. performed extraordinarily, even though they are less-reputable among the researchers. On the other hand, some well-established and well-reputable spectrum-based distance descriptors such as the distance energy and Estrada index and the distance Laplacian & signless Laplacian energies and Estrada indices, could not perform up to their reputation among chemical graph theorists and theoretical chemists.
Practically speaking, topological descriptors having correlation coefficients less then 0.95 are not recommended for their usage in quantitative structure–activity and structure–property models. Having said that, the well-known spectrum-based descriptors such as the the distance energy and the distance Estrada index, the Laplacian & signless Laplacian energies and Estrada indices, the Szeged and Schultz energies and Estrada indices etc. have correlation coefficients lower than 0.95 which is considered very poor from application perspectives. They should not be suggested for the quantitative structure–activity and structure–property models.”For their use in structure–property relationship models, we prefer the newly defined second atom-bond connectivity Estrada index and the Harary energy which have both of the correlation coefficients grater than 0.95. Despite their popularity, the results warrant further usage of the second atom-bond connectivity Estrada index and the Harary energy in the quantitative structure–activity and structure–property models.””Next, we exhibit the scatter plots of best five spectrum-based distance descriptors with normal boiling point and enthalpy of formation for the selected 22 lower benzenoid hydrocarbons. Tables 6 and 7 depict these scatter plots and the corresponding linear regression models. This explains the data dispersion and the error between the exact and correlated data points.””In conclusion, for their use in structure–property relationship models, we prefer only the second atom-bond connectivity energy and the Harary energy which have both of the correlation coefficients grater than 0.95. Despite of their popularity, the results warrant further usage of the second atom-bond connectivity index in the structure–activity and structure–property models.”
5 Applications to carbon polyhex nanotubes
When the size of molecular structures reduces to the range 1–100 nm, the study of nanotechnology starts. Having potential applications in computer science, electronics and medicine, nanotechnology creates many new devices and materials. Carbon nanotubes (CNTs) are cylindrical nano-skeletons comprising allotropic carbon. Carbon nanotubes have been found to possess relatively more applicative potential than their other counterparts.
The family of carbon polyhex nanotubes are the ones whose cylindrical surface is encompasses by hexagonal tessellation. Carbon polyhex nanotubes possess extraordinary stability for their existence in nature and, therefore, CNTs have fascinating thermal, electrical and mechanical characteristics (Dresselhaus et al., 1996). These significantly distinctive features of carbon polyhex nanotubes make these nanotubes the most studied nanostructures so far. Based on chirality, carbon polyhex nanotubes consist of different shapes such as zigzag, armchair and chiral etc. Fig. 5 depicts the zigzag and armchair structures of carbon polyhex nanotubes.3D view of zigzag and armchair polyhex nanotubes.
In order to study spectrum-based topological descriptors, we construct 2D graphs of these zigzag and armchair carbon polyhex nanotubes. Denoted by
, the zigzag polyhex nanotube is parameterized having m (resp. n) to be the number of hexagons in a row (resp. column). Similarly, the armchair polyhex nanotube is denoted by
, where the parameter m (resp. n) is defined to be the number hexagons in a fixed row (resp. column). Just for notational convenience, we denote an (
)-dimensional zigzag (resp. armchair) nanotube by
(resp.
). Fig. 6 exhibits the (
)-dimensional zigzag and armchair polyhex nanotubes.An (
)-dimensional zigzag and armchair polyhex nanotubes.
In this section, we employ our computational technique from Section 3 to calculate five best spectrum-based distance descriptors in Table 4 for carbon polyhex nanotubes. We choose two infinite families of zigzag polyhex nanotubes i.e.
with
and
. The remaining cases could be dealt similarly. Table 8 shows the calculations obtained for the zigzag polyhex nanotube
for
, as
is trivial.
43.8381
88.7005
47.4519
257.867
49.5709
63.559
133.8048
71.2886
401.5943
75.1084
82.6064
183.1969
96.6383
545.7397
100.7379
101.5198
233.275
122.1839
689.7301
126.3356
120.2328
285.5317
148.5081
834.0704
152.0197
138.8429
338.4085
174.9923
978.1854
177.6372
157.4242
390.6616
201.2161
1122.248
203.2384
175.9131
443.3483
227.7947
1266.368
228.8763
194.3108
497.784
254.7359
1410.176
254.4346
Next we use the cftool of MatLab on data in Table 8. cftool is a tool for curves and surface fitting in MatLab. We use R2013a version of the MatLab in our approximations. Our MatLab program generated the following results with 95% confidence intervals of coefficients: These results will help in correlating the -electronic energies of with significantly higher accuracy.
We also use our computational method in Section 3 to compute the best five spectrum-based topological descriptors exhibited in Table 4 for
nanotube. Table 9 shows the calculations obtained for the zigzag polyhex nanotube
for
, as
is trivial.
51.3551
110.9939
58.7608
321.2256
60.9452
74.8782
167.4179
88.1407
500.9904
92.5372
98.0492
224.7084
118.087
680.0174
123.9716
120.8667
285.951
149.2641
859.7601
155.5456
143.5718
349.1024
181.1978
1039.418
187.1002
166.1828
412.4662
213.212
1218.892
218.6333
188.6876
477.1917
245.5984
1398.273
250.135
211.1483
542.4422
278.1935
1577.927
281.6863
233.5527
608.1185
310.9007
1757.272
313.1939
Next we use the cftool on data in Table 9 for curve fitting purpose. Our MatLab program generated the following results with 95% confidence intervals of coefficients:
These results will help in correlation the -electronic energies of with significantly higher accuracy.
6 Applications to one-hexagonal carbon nanocones
Carbon nanostructures are among those organic structures which possess a fascinating phenomenon of the occurrence of hollow carbon structures. Other than nanotubes and fullerenes, carbon nanocones are observed as nano-caps at the ends of a nanotube. They could also be observed as a free-standing structure on a flatten-up graphite surface. Extraction of a fan from a graphite sheet, rolling the remaining sector about its apex and then joining the two open sides would normally generate a carbon nanocone structure. Especially, when the angle of apex becomes more than 60∘, a hexagon appears at the top of the apex of the nanocones. One-hexagonal nanocone is a carbon nanocone, which has a hexagon on the tip of its apex, called its core. Fig. 7 depicts two different 3D views of a one-hexagonal nanocone.3D views of a one-hexagonal nanocone.
We denote an n-dimensional one-hexagonal nanocone by
, where n is the number of hexagonal layers covering up the conical surface of the nanocone. Moreover, six in the subscript shows that the core of the nanocone is a hexagon. Fig. 8 depicts the 3-dimensional
nanocone.The 3-dimensional
nanocone.
We also use our computational method in Section 3 to compute the best five spectrum-based topological descriptors exhibited in Table 4 for one-hexagonal nanocone
. Table 10 shows the calculations obtained for the one-hexagonal nanocone
for
.
8.9796
13.6967
8.0000
29.3333
7.3333
28.7419
61.9253
33.0350
166.0818
32.6030
58.4033
151.0953
77.5585
410.3461
75.8024
100.6909
274.9440
139.3883
760.2151
136.6019
154.8825
436.5923
219.4629
1215.343
1215.343
221.0308
632.9817
317.2058
1776.411
310.9049
299.4101
855.8344
429.0025
2443.636
424.5764
389.4633
1121.645
562.2183
3217.493
556.0342
491.3982
1432.679
716.7887
4097.644
705.2066
605.4201
1772.087
886.2247
5083.353
871.9638
By using R2013a version of the MatLab, we employ cftool on data in Table 10. Our MatLab program generated the following results with 95% confidence intervals of coefficients: These results will help in correlation the -electronic energies of one-hexagonal nanocones with significantly higher accuracy.
7 Conclusion
7.1 Contributions
The following are the main contributions of this paper:
-
We propose a computational method to calculate commonly occurring spectrum-based distance descriptors.
-
Experimental results show that our proposed method possesses less computational complexity and is more computationally diverse.
-
The proposed method is used to calculate commonly occurring spectrum-based distance descriptors to investigate their correlation ability with the experimental data for the two chosen physicochemical properties.
-
Some favorable and some unexpected outcomes have been reported based on the quality testing.
-
Our study contributes towards putting forward the best spectrum-based topological descriptors and meanwhile mentioning the ones which do not deserve further attention of researchers.
7.2 Implications
The second ABC Estrada index has outperformed all of the well-known spectrum-based distance descriptors. Unlike their reputation among researchers, the harmonic and degree-distance energies also secured spots in the list of best five spectrum-based distance descriptors.
The newly defined second GA energy and Estrada index both secured 3rd and 4th positions in the priority list. This implies that the newly introduced spectral descriptors based on the second ABC and the second GA matrices has performed very well. The results warrant further usage of these newly introduced spectrum-based distance descriptors in the structure–activity and structure–property models. The study also warrants that the well-studied distance energy, the distance Estrada index and the distance Laplacian & signless Laplacian energies and Estrada indices do not deserve as much attention of the researchers as they do in the literature.
7.3 Limitations
The following are the main limitations of this study:
-
The study is restricted to correlating physicochemical properties only. Structural & surface properties and molecular formations cannot be correlated by using the class of distance-based distance descriptors.
-
The current study is only applicable to aromatic hydrocarbons. Thus, it is restricted to be applied to non-aromatic and anti-aromatic hydrocarbons and their derivative.
-
There might exist other graph-theoretic topological descriptors having better correlations with various physicochemical properties than these spectrum-based valency descriptors. For instance, one could investigate the class of counting related descriptors (Hosoya, 1988).
7.4 Future study
Based on limitations of this study, it is natural to investigate further research directions in this area. In the quest of finding the best graph-theoretic topological descriptors, we propose to:
-
Investigate predictive potential of graph-theoretic descriptors for determining the structural and atomic configuration related properties of hydrocarbons.
-
Investigate predictive potential of counting related descriptors (Hosoya, 1988) for estimating various physicochemical properties of benzenoid hydrocarbons.
-
Can this study be extended to non-aromatic and anti-aromatic hydrocarbons?
Declarations
Availability of data and materials
The data associated with this manuscript is available in a public repository on GitHub accessible via https://github.com/Sakander/Distance-based-spectral-descriptors.git.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
CRediT authorship contribution statement
Sakander Hayat: Conceptualization, Methodology, Software, Writing- reviewing and editing. Suliman Khan: Data curation, Investigation, Visualization, Writing- original draft preparation. Muhammad Imran: Supervision, Project administration, Funding acquisition.
Acknowledgements
S. Hayat and M. Imran were supported by the University Programme for Advance Research (UPAR) grant of United Arab Emirates University under Grant No. G00003271. S. Hayat is also supported by the Higher Education Commission, Pakistan under Grant No. 20–11682/NRPU/RGM/R&D/HEC/2020. We would like to express our sincere gratitude to the reviewer for his/her helpful comments which have played a vital role in improving the quality and presentation of the original manuscript.
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