Journal of Molecular Structure (Theochem) 466 (1999) 211217

Chemical graphs and their basis invariants

M.I. Skvortsova a, I.I. Baskin a, L.A. Skvortsov a, V.A. Palyulin b, N.S. Zefirov b,
I.V. Stankevich c,*
a
N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky Prosp. 47, Moscow 117819, Russia
b
Department of Chemistry, Moscow State University, Moscow 119899, Russia
c
A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Science, Vavilov Str. 28, Moscow 117813, Russia
Received 25 June 1998; accepted 26 August 1998

Abstract
Molecular graph invariants are often used as molecular descriptors in structure-property correlations. There exists an
infinite number of graph invariants. Most of them are constructed using refined mathematical operations with graphs and
cannot be easily interpreted in structural or physico-chemical terms. So, the problem of the choice of molecular descriptors in
structure-property correlation appears. It is known that many invariants are related to each other by strict or approximate
formulas. Thus, these descriptors reflect the same features of molecular structures. So, the following problem appears: for any
finite set of molecular (or arbitrarily labeled) graphs, to find a finite set of basis invariants, such that any invariant of these
graphs could be uniquely expressed as a linear combination of basis invariants. A solution of the above-mentioned problem and
some examples are presented in the given paper. q 1999 Elsevier Science B.V. All rights reserved.
Keywords: Molecular graphs; Graph invariants; Topological indices; Basis of graph invariants; Structural fragments; Fullerenes

1. Introduction some numbers in the procedure of calculation of the

The search for structure-property relationships is
an important problem of contemporary chemistry.
The methods of molecular description play an essen-
tial role in these investigations. One of the most popu-
lar such methods is based on representing molecular
structure as a labeled graph and using graph invariants
[15] for its characterization. An invariant of a
labeled graph is, accordingly to definition, any
number, calculated from a graph, which does not
depend on numbering the graph vertices. This
means that graph labels must be transformed into
* Corresponding author.
E-mail address: stan@ineos.ac.ru (I.V. Stankevich)
0166-1280/99/$ - see front matter q 1999 Elsevier Science B.V. All rights reserved.
PII: S0166-128 0(98)00467-9
invariant.
Note that there exists an infinite number of graph
invariants. Therefore, in the search for structure-
property correlation, the problem of choice of invar-
iants and type of functional dependence between
invariants and property appears. However, the justi-
fied choice of molecular graph invariants is not always
possible, since they are often constructed using
refined mathematical operations with graphs and
cannot be easily interpreted in structural or physico-
chemical terms.
It is known, that many graph invariants are related
to each other by strict or approximate mathematical
formulas. Thus, these molecular descriptors reflect the
same features of molecular structures. So, the follow-
ing theoretical problem appears: for any finite set of
212 M.I. Skvortsova et al. / Journal of Molecular Structure (Theochem) 466 (1999) 211217
labeled graphs, to find a finite set of basis invariants,
such that any invariant of these graphs could be
uniquely expressed as a linear combination of basis
invariants. In the case of the existence of basis invar-
iants, one can choose molecular topological descrip-
tors from this basis and use only a linear kind of
functional dependence in the graph invariants-prop-
erty relationships.
In this paper, a basis of invariants of labeled graphs
from any finite set is found. It is proven, that invar-
iants, which are equal to the occurrence numbers of
some subgraphs into a graph, form such a basis. A
technique of expansion of an invariant on the basis
is illustrated by a simple example. The results of
expansion of 25, arbitrarily selected, well-known
invariants on the basis for a set of 10 chemical struc-
tures, also arbitrarily selected, are given.
2. Main results
Let Gi (i 1,,N) be some finite set of vertex and
edge labeled non-isomorphic graphs with arbitrary
labels, and Hj (j 1,,N) be some set of subgraphs
of these graphs. (Note, that a subgraph of a graph is
obtained by deleting some vertices, edges in a given
graph, with, probably, further deleting some labels).
Denote by gj gj(G), the graph invariant, which is
equal to the occurrence number of Hj into G, by bij
gj(Gi) and by B (bij) for the corresponding matrix
(i,j 1,,N).
Theorem. 1) There exists such a set of subraphs Hj
(called basis subgraphs) of the given graphs Gi (i,j
1,,N) so that detB 0.
2) The corresponding invariants gj (j 1,,N)
form a finite basis of invariants of Gi (i 1,,N) in
the sense, that any invariant, f, of these graphs is
uniquely represented in the following form:
f G a1 g1 G 1 a2 g2 G 1 1 aN gN G 1 their labels only (but not vertices and not labels).
where aj (j 1,,N) are some constants independent
on G and dependent on f only.
3) In Eq. (1), one can take any basis f (f1,,fN)
obtained from g (g1,,gN) by means of transforma-
tion f Ag, where A is any non-singular square N N
matrix, and f and g are vector-columns.
Proof. 1) Show that one can take Hj Gj (j
1,,N). Order Gj in decreasing numbers of vertices
and edges (graphs with the same numbers of vertices
and edges may be ordered arbitrarily). Then bij
gj(Gi) 1 for i j, and bij gj(Gi) 0 for i . j.
Hence, B is an upper-triangular matrix with units on
the diagonal, and detB 1. Thus, the chosen
subgraphs Hj (j 1,,N) satisfy the condition
detB 0.
2) Write Eq. (1) for all G Gi (i 1,,N):
f Gi a1 g1 Gi 1 a2 g2 Gi 1 1 aN gN Gi 2
To prove the statement from Part 2 of the theorem,
it is necessary and sufficient to prove that the system
of equations (Eq. (2)) for unknown parameters a
(a1,,aN) has an unique solution for any numbers y
(f(G1),,f(GN)). Write Eq. (2) in the matrix form: y
Ba. Since B is a non-singular matrix, this equation has
an unique solution of kind a B 21y.
3) Substitute fj for gj (j 1,,N) in Eq. (1). Repeat-
ing the mathematical treatment from Part 2, we obtain
the system of equations in a matrix form: y Fa,
where F (fij) (fj(Gi)), i,j 1,,N, F AB,
detF detAdetB 0. Analogously, this matrix
equation has an unique solution of the kind a
F 21y. The theorem is proven.
3. Remarks
It follows from the proof of the theorem, that one
can take as a basis any set of invariants gj (j 1,,N),
for which detB 0, where B (bij) (gj(Gi)), gj(Gi)
are values of gj on Gi (i 1,,N).
The particular case of the theorem was considered
in Ref. [6], where it was supposed that: (a) a given set
of graphs consists of all graphs with one and the same
fixed vertex number n, labels of vertices and edges are
chosen from two arbitrary finite symbol sets V and E,
respectively; (b) any subgraph may be obtained from
the given graph by deleting some edges, together with
4. Examples
Example 1
Here we illustrate on simple graphs, subgraphs
 M.I. Skvortsova et al. / Journal of Molecular Structure (Theochem) 466 (1999) 211217 213

are:
0 1 0 1
1 0 0 1 0 0
B C 21 B C
Fig. 1. Graphs G1, G2, G3 and their subgraphs H1, H2, H3, considered BB
@3 3 0C B
A; B @ 21 1=3 0 C
A
in Exmple 1.
4 4 4 0 21=3 1=4
P
Consider a set of graph invariants k f vki , where
and invariants a technique of finding the expansion vi is the degree of ith graph vertex and k is any fixed
coefficients aj (j 1,,N) in Eq. (1). Consider number. Then: k f G1 2, k f G2 32k and
three non-labeled graphs G1, G2, G3 and their
k
f G3 2k12 . It was shown (see proof of theorem),
subgraphs H1, H2, H3 pictured in Fig. 1, and that expansion coefficients a (a1,a2,a3) on the basis
corresponding invariants g1, g2, g3. In this case, g1,g2,g3 are calculated by the formula: a B 21y,
the non-singular matrix, B, of occurrence numbers y k f G1 ; k f G2 ; k f G3 . So, in this case a1 2,
Hj into Gi (i,j 1,2,3) and inverse matrix, B 21, a2 2 k 2 2, a3 0 and k f 2g1 1 2k 2 2g2 .

Fig. 2. Molecular graphs G1 G10, considered in Example 2.

214 M.I. Skvortsova et al. / Journal of Molecular Structure (Theochem) 466 (1999) 211217

Fig. 3. Subgraphs H1 H10 of graphs pictured in Fig. 2.

Table 1
Values of selected 25 graph invariants for 10 molecular graphs pictured in Fig. 2

G1 G2 G3 G4 G5 G6 G7 G8 G9 G10

(1) 1 x 10.003 9.651 13.059 9.357 12.401 10.507 9.631 10.395 13.223 9.651
(2) 1 xv 8.184 6.571 10.123 6.820 8.749 7.838 5.943 8.005 10.817 6.961
(3) 3 xc 2.194 1.182 2.338 2.394 2.103 2.082 1.665 2.310 1.211 1.182
(4) 3 xvc 1.622 0.460 1.626 1.601 0.846 1.374 0.566 1.635 0.814 0.492
(5) 3 xp 9.173 6.824 11.273 7.368 8.907 8.836 8.052 7.951 9.265 6.824
(6) 3 xvp 6.683 3.224 7.594 4.080 4.614 5.310 3.290 4.821 6.109 3.502
(7) 1 k 14.583 16.371 18.992 16.371 20.727 16.843 13.648 18.340 21.702 16.371
(8) 2 k 5.000 7.852 7.356 6.405 9.000 6.481 5.025 7.713 11.253 7.852
(9) 3 k 2.066 4.250 3.238 3.442 4.716 2.810 2.203 4.110 5.990 4.250
(10) 1 ka 13.741 14.253 17.355 14.693 18.237 15.195 11.511 16.912 20.317 14.507
(11) 2 ka 4.546 6.328 6.402 5.348 7.358 5.488 3.844 6.758 10.213 6.506
(12) 3 ka 1.839 3.251 2.735 2.767 3.693 2.286 1.590 3.498 5.310 3.366
(13) 1 IC 2.672 2.268 2.822 2.719 2.556 2.763 2.900 2.634 2.447 2.395
(14) 1 TIC 120.265 86.201 149.609 108.798 122.709 121.611 81.221 126.472 137.046 95.818
(15) 1 SIC 0.486 0.432 0.492 0.511 0.457 0.506 0.603 0.471 0.421 0.450
(16) 1 BIC 0.478 0.429 0.483 0.507 0.452 0.500 0.585 0.469 0.417 0.447
(17) 1 CIC 2.819 2.979 2.905 2.601 3.028 2.695 1.906 2.950 3.360 2.926
(18) 3 IC 5.030 3.997 5.194 4.596 4.730 4.890 4.593 4.772 4.838 3.984
(19) 3 TIC 226.378 151.911 275.315 183.857 227.058 215.195 128.605 229.058 270.947 159.367
(20) 3 SIC 0.916 0.761 0.906 0.863 0.846 0.895 0.955 0.854 0.833 0.748
(21) 3 BIC 0.900 0.756 0.890 0.857 0.838 0.885 0.927 0.849 0.825 0.743
(22) 3 CIC 0.461 1.250 0.533 0.725 0.854 0.568 0.214 0.812 0.969 1.337
(23) W 826 814 1819 788 1722 977 726 1045 1896 814
(24) n 45 38 53 40 48 44 28 48 56 40
(25) MW 288.388 266.340 366.458 272.345 350.415 298.383 268.226 302.415 429.398 268.356
 M.I. Skvortsova et al. / Journal of Molecular Structure (Theochem) 466 (1999) 211217 215

Table 2
The expansion coefficients aj on basis gj (j 1,,10) for selected 25 graph invariants

a1 a2 a3 a4 a5 a6 a7 a8 a9 a10

(1) 1 x 2 0.110 0.774 2 0.549 0.210 0.355 2 3.362 0.648 2 0.323 2 1.207 0.999
(2) 1 xv 0.129 0.714 2 0.490 0.265 0.660 2 5.597 2 0.037 0.610 2 5.585 0.549
(3) 3 xc 2 0.083 0.172 2 0.192 0.003 0.373 2 0.506 0.298 2 0.578 2.335 0.153
(4) 3 xvc 0.026 0.128 2 0.185 0.072 0.388 2 0.874 2 0.003 2 0.097 2 0.322 0.038
(5) 3 xp 0.861 0.136 0.229 2 0.077 0.690 2 2.988 0.224 0.649 2 3.208 0.502
(6) 3 xvp 0.646 0.109 0.176 0.021 0.821 2 4.578 2 0.303 1.048 2 5.877 0.115
(7) 1 k 2 2.170 2.175 2 2.221 0.816 2 0.255 2 2.617 1.557 2 3.194 3.939 2.130
(8) 2 k 2 1.479 1.299 2 1.503 0.679 2 0.478 2 1.816 0.439 2 1.249 2 1.197 1.095
(9) 3 k 2 1.200 0.971 2 1.258 0.531 2 0.295 2 1.072 0.279 2 1.092 0.776 0.684
(10) 1 ka 2 1.681 2.094 2 2.188 0.913 0.272 2 5.464 0.955 2 2.342 2 1.245 1.746
(11) 2 ka 2 0.980 1.174 2 1.377 0.692 0.003 2 3.988 0.036 2 0.501 2 4.876 0.792
(12) 3 ka 2 0.792 0.837 2 1.092 0.504 0.026 2 2.418 0.027 2 0.518 2 1.783 0.469
(13) 1 IC 0.606 0.084 0.041 2 0.036 0.259 2 0.858 2 0.201 0.454 2 1.420 0.083
(14) 1 TIC 2 5.511 12.587 2 7.352 1.636 2 7.497 9.186 7.704 2 0.037 14.619 8.207
(15) 1 SIC 0.158 0.003 0.017 2 0.009 0.078 2 0.243 2 0.058 0.117 2 0.401 0.007
(16) 1 BIC 0.149 0.06 0.014 2 0.008 0.071 2 0.222 2 0.056 0.109 2 0.370 0.009
(17) 1 CIC 2 0.328 0.372 2 0.425 0.223 2 0.111 2 0.522 2 0.037 2 0.829 2 0.350 0.372
(18) 3 IC 0.822 0.161 2 0.110 0.114 1.019 2 4.250 2 0.327 0.134 2 4.641 0.226
(19) 3 TIC 2 13.758 22.166 2 20.553 10.920 17.577 2 130.956 11.717 2 19.351 2 104.870 16.322
(20) 3 SIC 0.225 0.010 2 0.002 0.016 0.233 2 0.899 2 0.094 0.073 2 1.055 0.03
(21) 3 BIC 0.210 0.014 2 0.007 0.017 0.222 2 0.861 2 0.091 0.060 2 1.003 0.033
(22) 3 CIC 2 0.545 0.294 2 0.273 0.072 2 0.871 2.869 0.088 2 0.508 2.870 0.229
(23) W 2 427.283 152.658 2 127.593 9.462 2 46.809 2 214.154 430.343 2 123.930 1525.733 177.723
(24) n 2 4.619 5.890 2 5.401 2.422 2 1.865 2 7.474 1.775 2 6.178 2 4.122 4.379
(25) MW 25.657 20.435 2 18.357 12.185 72.295 2 384.664 2 10.420 39.717 2 368.508 20.498

Example 2 Since detB 0, invariants gj (j 1,,10) form a

finite basis of invariants of graphs Gi (i 1,,10),
Consider 10 structures Gi (i 1,,10), in Fig. 2 that is, any invariant of these graphs may be uniquely
and 10 of their substructures Hj (j 1,,10), in Fig. 3. represented in Eq. (1).
Find matrix B (bij), where bij gj(Gi) is equal to Consider 25 well-known graph invariants (see the
the occurrence number of Hj into Gi (i,j 1,,10): first column of Table 1): (a) six indices of molecular
connectivity of order 1 and 3, both simple and
0 1
1 24 33 43 7 1 0 1 1 3 weighted [7,8]: 1 x, 1 xv , 3 xc , 3 xvc , 3 xp , 3 xvp ; (b) six
B C kappa-indices of order 1, 2 and 3, both simple and
B2 8C
B 4 3 2 0 0 0 0 0 C
B C taking into account the presence of heteroatoms and
B C
B1 24 34 46 7 1 2 2 1 5C multiple bonds [912]: i k, i ka (i 1,2,3); (c) ten
B C
B C information topological indices of order 1 and 3
B1 13 10 7 5 1 0 0 0 5C
B C [13,14]: k IC, k TIC, k SIC, k BIC, k CIC (k 1,3); (d)
B C
B2 7C
B 9 7 4 1 0 2 0 0 C Wiener index W [15]; (e) number of atoms, n; and (f)
BB
B
C
C molecular weight, MW. The values ot these 25 invar-
B1 16 16 14 5 1 1 0 0 5C
B C iants for Gi (i 1,,10) are given in Table 1, with the
B C
B4 7C expansion coefficients aj (j 1,,10) on the basis of
B 3 1 0 0 0 2 0 0 C
B C gj (j 1,,10) for them, in Table 2.
B C
B1 16 14 13 5 1 1 0 0 4C
B C
B C
B1 11 11 12 1 0 2 1 0 7C
@ A Example 3
2 6 4 2 0 0 0 0 0 7 Consider three polyhedral carbon clusters:
216 M.I. Skvortsova et al. / Journal of Molecular Structure (Theochem) 466 (1999) 211217

Fig. 4. Molecular graphs G1, G2, G3, corresponding to fullerene (Ih)-C60 and two of its isomers; H1, H2, H3-basis subgraphs for the set G1, G2, G3.
 M.I. Skvortsova et al. / Journal of Molecular Structure (Theochem) 466 (1999) 211217
fullerene (Ih)C60 and two of its isomers obtained by
using one or three of the StoneWales transforma-
tions [16]. The Schlegel graphs Gi (i 1,2,3) of
these molecules and three selected subgraphs, Hj (j
1,2,3) are shown in Fig. 4 (all pentagons are marked
by the symbol 5). In this case, the non-singular
matrix, B, is:
0 1
12 0 0
B C
BB @ 12 2 0 A
C a structure-property equation of kind Eq. (1), which
12 5 1
Therefore, subgraphs Hi (i 1,2,3) are basis ones
and the arbitrary invariant of considered molecular
graphs is represented as a linear combination of corre-
sponding basis invariants.
Consider the parameter DE, the difference between
LUMO and HOMO energies. Then, DE(G1) 0.756,
DE(G2) 0.3184, DE(G3) 0.05. This graph invar-
iant may be represented in the following form: DE
0.063g1 2 0.219g2 1 0.347g3.
5. Conclusions
It is proven that any graph invariant for any finite
set of labeled graphs can be uniquely represented as a
linear combination of occurrence numbers of some
substructures (fragments) which may be both
connected and disconnected, both labeled and
partially labeled. Thus, the corresponding invariants
form a finite basis of invariants of graphs of the
considered set.
It follows from the proof of theorem that there
exists an infinite number of basis sets of invariants.
However, the basis related with the occurrence
numbers of fragments is more convenient for applica-
tion, since these molecular parameters have a natural
structural interpretation.
It follows from the theorem, that different graph
invariants differ from each other by choice of the
coefficients, aj, in expansion of them on basis [see
Eq. (1)]. This formula allows the automatic construc-
tion of an infinite set of graph invariants; coefficients
aj may depend on the structures of corresponding
subgraphs.
One can consider the result discussed as the strict
mathematical justification of the use of well-known
217
additive methods for calculating different properties
of chemical compounds.
Suppose, that some structure-property equation of
kind y F(x1,,xL) (xi are some graph invariants, y
is the property value, and i 1,,L) is obtained using
a training set of compounds K1, and it is applied for
estimation of the properties of compounds from a test
set K2. One can consider y as some invariant of the
graphs from the union of K1 and K2. Then there exists
gives the same (exactly!) predicted result for
compounds of K1 and K2. Evidently, this equation
will contain more parameters. However, this is not
essential in the frame of the set K1 and K2 , since
both models give the same result.
Our result is valid for any finite set of labeled
graphs. However, this limitation is not essential in
applications, since any chemical task deals with
only a finite set of chemical compounds.
Acknowledgements
The authors thank the Japan Society for Promotion
of Science and the Russian Foundation for Basic
Research.
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