ESI-3D: Electron Sharing Indexes Program for 3D Molecular

Space Partition

Institute of Computational Chemistry (Girona), 2006.

Report bugs to Eduard Matito: eduard@iqc.udg.es or ematito@gmail.com

The Electron Sharing Indexes (ESI)

The electron sharing indexes (ESI) account to some extent for the electron
sharing of a given pair of atoms. The ESI computed with this program are calculated
from the exchange correlation density (XCD),1 which reads as follows:

xc ( x 1 , x 2 ) = (1) ( x 1 ) (1) ( x 2 ) (2 ) ( x 1 , x 2 ) (1)

and measures the divergences of the pair density, (2 ) ( x1 , x 2 ) , a true electron pair
distribution, and a fictitious pair density constructed as the product of two
independent one electron distributions, (1) ( x1 ) (1) ( x 2 ) . Therefore, the XCD integrates
to N, since the density and the pair density integrate to N and N(N-1), respectively:

xc ( x 1 , x 2 ) dx 1 dx 2 = N
(2)

The XCD is an appealing function because it fulfills several interesting properties. First
of all, it is non-negative definite; the number of fictitious pairs of electrons for a model
of independent electrons is always greater than the actual number of pairs. Secondly, by
definition, in the case of non-interacting electrons the function is zero. And in third
place, integrated over the whole space, it gives the number of electrons in the system, N,
which enables a chemical meaningful molecular space decomposition of the N electrons
of a given system.

For a single determinant wave function (Hatree-Fock, or a Kohn-Sham orbitals

one) the pair density can be written in terms of the first order reduced density matrix (1-
RDM):

(1) (x1 x1 ) (1) (x1 x 2 )

r r r r
rr
(2 )
(x1 x2 ) = (1) r r
(x 2 x1 ) (1) (x 2 x 2 )
r r (3)
where (1) (x1 x 2 ) is the first order reduced density matrix (1-RDM) which for the case
r r
r r
x1 = x 2 reproduces the density. Thus simplifying the expression of the XCD to read:

xc ( x1 , x2 ) = (1) (x2 x1 )
r r r r 2
(4)

In 1975, Bader and Stephens2 pointed out that the integration of the XCD upon
two different regions of the space A and B leads to a measure of the correlative
interactions between the electrons in these two moieties. However, it was not Bader the
first to propose such a quantity as an ESI. In 1993 Fulton3 proposed an ESI based in the
framework of the QTAIM by using the 1-RDM in following manner:

r r r r r r
( A, B ) = 2 (1) (x1 ; x2 )[1 / 2 ] (1) (x2 ; x1 )[1 / 2]dx1dx2 , (5)
AB

whereupon the pseudo-square root of the 1-RDM reads

r r r r
(1) ( x1 ; x 2 )[1 / 2 ] = 1k/ 2 k* ( x1 ) k ( x 2 ) , (6)
k

k and k(x) being the natural occupancies and natural spin orbitals, respectively. It is
more convenient to express Eq. (5) in following manner:

( A, B ) = 2 1i / 2 1j/ 2 S ij ( A) S ij ( B ) , (7)
ij

Sij(A) is the diagonal element of the atomic overlap matrix (AOM) in terms of natural
spinorbitals integrated over the domain of atom A:

r r r
S ij ( A) = i ( x1 ) j ( x1 )dx1 (8)
A

For single determinant methods Eq. (7) simplifies to:

( A, B ) = 2 S ij ( A) S ij ( B ) , (9)
ij

where Sij(A) now corresponds to the AOM in terms of spinorbitals. For

monodeterminantal wave functions it coincides with later definitions given by ngyan4
or by Fradera5 for the quantum theory of atoms in molecules (QTAIM) partition of the
molecular space into atomic domains.6 Fradera et al.5 also proposed the localization
index as:

( A, A)
( A) = = S ij ( A) S ij ( A) , (10)
2 ij

Chemically interesting can be also the atomic delocalization which is simply

calculated as follows:

( A) = ( A, B ) , (11)
B A

and some authors recognize this quantity as the atomic valence.7 Finally is worth
noticing that these XCD based ESI can be calculated from different partitions. The first
partition attempted to calculate this index was reported by Wiberg8 for a Mulliken-like
decomposition.9 This program has been designed to deal with any AOM properly
formatted. In particular we have adapted the AIMPAC format,10 which is also the
format of FUZZY package.11 Therefore, by using the *.int files generated by these
programs, one can calculate QTAIM-ESI and FUZZY-ESI respectively.12

The program is prepared for the calculation of unrestricted and restricted single
determinant ESI. In addition, the program provides the possibility of splitting the ESI
according to orbital contributions. In general the ESI can be decomposed as follows:

( A, B ) = S ij ( A)S ij (B ) = i ( A, B ) (12)
i j i

which may give further inside in the orbital contribution to the chemical bonding.13 In
general an exact orbital decomposition is done for those cases where Sij(A)=0 when i
and j belong to different sets of orbitals. This is the case of - separation of a planar
molecule. In the cases where the decomposition is not exact it is explicitly indicated in
the output.

For an extensive revision of these quantities check for example reference 14.
Aromaticity Indexes: FLU and PDI

From these ESI the calculation of the aromaticity indexes PDI15, 16 and FLU17 is
also possible with ESI-3D. The PDI is a specific measure of local aromaticity for six
member rings (6-MRs), where three para-related positions exist, namely (1,4), (2,5),
and (3,6). By definition, the PDI of a 6-MR is given by:

(1,4) + (2,5) + (3,6)

PDI = (13)
3

While the FLU index of aromaticity reads:

( A, B ) ref ( A, B )
2
1 RING ( B )
FLU = , (14)
n A B ( A)
( A, B )

ref

where the summation runs over all adjacent pairs of atoms around the ring, n is equal to
the number of atoms of the ring, ref ( A, B ) is the ESI for the atomic pair A and B from
the aromatic molecule chosen as a reference, and is a constant to ensure the ratio of
atomic valences is greater than one,

1 ( B) > ( A)
= (15)
1 ( B) ( A)

The program recognizes the bonds C-C, C-N and B-N for which it takes the reference
parameters from benzene, pyridine and borazine, which are respectively 1.4, 1.2 and
0.86, for QTAIM, and 1.4, 1.5 and 1.63 for FUZZY partitions. If the bond is not
recognized the program uses C-C value by default and gives a warning message.

The program needs for atomic overlap matrices according to the format of FUZZY11 or
AIMPAC10 programs;18 both programs are also freeware. When the orbitals are
decomposed into two groups the program attempts the calculation of PDI and FLU.

For a recent review on electronic aromaticity indexes check reference 19.

Accuracy

In order to check the accuracy of the calculation one must check that that the
sum rule is fulfilled:

1
2 (A , A ) + ( A ) = 2 ( A ) + ( A ) = N ( A )
1
i j i i i i =N (16)
i j i i i

It is of recommendable practice to ensure the accuracy achieved for N to be at least 10-3

electrons. Since the indexes are calculated from the AOM in Eq. (8), it is also
recommendable that the following quantity:

Error ( S ) = S ij ( A) ij (17)
ij A

never increases over 10-3. Additionally AIMPAC program gives the value of the
laplacian of the density within a basin. For an accurate calculation this value is usually
below 10-3.

Quotation

Program: E. Matito, in 'ESI-3D: Electron Sharing Indexes Program for 3D

Molecular Space Partition.' Girona, IQC, 2006.

PDI index: J. Poater, X. Fradera, M. Duran, and M. Sol, Chem. Eur. J.,
2003, 9, 400.

FLU index: E. Matito, M. Duran, and M. Sol, J. Chem. Phys., 2005,

122, 014109.

PDI or FLU from FUZZY-partition: E. Matito, P. Salvador, M. Duran, and

M. Sol, J. Phys. Chem. A, 2006, 110, 5108.

Usage

ESI.x file.in

Tests: test.x

Downloads

ESI-3D: http://iqc.udg.es/~eduard/ESI-3D/
FUZZY: http://iqc.udg.es/~eduard/ESI-3D/
AIMPAC: http://www.chemistry.mcmaster.ca/aimpac/
Keywords

$ATOMS. Number of atoms and files containing the overlap matrix for each atom.
PROAIM (AIMPAC) or FUZZY format expected.

$ATOMS
number of atoms (n)
file_1.int
file_2.int
...
file_n.int

$BASIS. The number of occupied molecular orbitals (or spinorbitals if open-shell).

$BASIS
number of occupied (spin)orbitals

$TYPE. Type of wave function, restricted- HF or KS wave function (hf) or unrestricted

one (uhf) expected. If uhf then the program reads the number of the first beta
spinorbital.

$TYPE
hf or uhf
(number of the first beta spinorbital)

$RING. Needed for the calculation of aromatic properties. Holds the information of the
connectivity of the ring(s). Important: the atoms of each ring must be specified
according to the connectivity of each ring.

$RING
number of rings (nr)
number of members in the first ring (nm1)
1 2 ... nm1 (the atom number according to their connectivity)
...
number of members in the n-th ring (nmn)
1 2 ... nmn

$GROUPS. Needed for the orbital decomposition of the ESI and the aromatic indexes.
First we must provide the number of groups, and afterwards the number assigned to
each orbital according to the group they belong. For separation of 5 occupied
orbitals it might read:

$GROUPS
2
11212

$FUZZY. When the program founds such keyword it uses the references of FUZZY-
ESI for the calculation of FLU.
Example

Benzene is given as an example of a molecule with a ring, whose decomposition

is attempted by different symmetry of occupied orbitals (benzene.esi.d6h), and
afterwards by doing the sigma-pi separation (benzene.esi.cs). Here below a brief
explanation:

INPUT:

$BASIS
21
$ATOMS
12
benze_C1.int
benze_C2.int
benze_C3.int
benze_C4.int
benze_C5.int
benze_C6.int
benze_H7.int
benze_H8.int
benze_H9.int
benze_H10.int
benze_H11.int
benze_H12.int
$TYPE
hf
$RING
1 rings found
6 members of 1th ring
1 2 3 4 5 6
$GROUPS
2
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 1 1 2 2

This input requests a single Slater determinant closed-shell calculation (hf) of

all ESI according to Eq. (9) and (10). Since the keyword $RING is specified, the
program will attempt the calculation of FLU, and providing the number of members in
the ring is six, he will also provide the PDI measure. ESI-3D will perform an orbital
analysis of the ESI based on the decomposition given. The FLU and PDI will be also
calculated because there are two groups of orbitals, 1 and 2, which will be supposed
and respectively.
OUTPUT

Population and ESI analysis: Eq. (10) Eq. (11)

-----------------------------------------------
| Atom N (int) loc. deloc. N1 N2
-----------------------------------------------
| C 1 6.0143 3.9563 4.1161 5.0386 0.9757
| C 2 6.0144 3.9563 4.1162 5.0386 0.9757
| C 3 6.0144 3.9563 4.1162 5.0386 0.9757
| C 4 6.0143 3.9563 4.1161 5.0386 0.9757
| C 5 6.0144 3.9563 4.1162 5.0386 0.9757
| C 6 6.0144 3.9563 4.1162 5.0386 0.9757
| H 7 0.9857 0.4437 1.0839 0.9614 0.0243
| H 8 0.9857 0.4437 1.0839 0.9614 0.0243
| H 9 0.9857 0.4437 1.0839 0.9614 0.0243
| H 10 0.9857 0.4437 1.0839 0.9614 0.0243
| H 11 0.9857 0.4437 1.0839 0.9614 0.0243
| H 12 0.9857 0.4437 1.0839 0.9614 0.0243
-----------------------------------------------
| - 0 41.9999 26.3998 31.2003 35.9999 6.0000
-----------------------------------------------

N(int) is the population given in the input files which contain the AOM (*.int)
N1 corresponds to the population of orbitals in group 1
N2 corresponds to the population of orbitals in group 2

Eq. (9)

--------------------------------------
| Pair DI DI1 DI2
--------------------------------------
| C 1-C 1 3.9563 3.5185 0.4378
| C 1-C 2 1.3993 0.9698 0.4295
| C 1-C 3 0.0727 0.0345 0.0382
| C 1-C 4 0.1009 0.0080 0.0929
| C 1-C 5 0.0727 0.0345 0.0382
| C 1-C 6 1.3993 0.9698 0.4295
| C 1-H 7 0.0041 0.0004 0.0036
| C 1-H 8 0.0079 0.0071 0.0007
| C 1-H 9 0.0439 0.0339 0.0100
......................................
| H 11-H 12 0.0050 0.0048 0.0002
| H 12-H 12 0.4437 0.4434 0.0003
---------------------------------------
| TOTAL: 41.9998 35.9999 6.0000
| LOCAL: 26.3998 23.7714 2.6284
| DELOC: 31.2001 24.4570 6.7431
---------------------------------------

TOTAL Total number of electrons calculated by Eq (16).

LOCAL Total localization
DELOC Total delocalization
 (B )
( A, B ) ref ( A, B )
ref ( A, B )
( A)
---------------------------------------------------------------------
| RING 1 - 6 bonds
| Atom pair delta i-->j j-->i Exc(i,j) diff Flu(i,j)
---------------------------------------------------------------------
| C 1-C 2 1.399 0.340 0.340 1.000 0.000 0.00000022
| C 2-C 3 1.399 0.340 0.340 1.000 0.000 0.00000019
| C 3-C 4 1.399 0.340 0.340 1.000 0.000 0.00000022
| C 4-C 5 1.399 0.340 0.340 1.000 0.000 0.00000022
| C 5-C 6 1.399 0.340 0.340 1.000 0.000 0.00000019
| C 1-C 6 1.399 0.340 0.340 1.000 0.000 0.00000022
| FLU 1 = 0.000000

( A, B ) ref ( A, B )
2
1 RING 1 RING ( B )
FLU = Flu (i, j ) =
n A B n A B ( A)
( A, B )

ref

---------------------------------------------------------------------
| 0.100936 0.100989 0.100989
| PDI 1 = 0.100972
---------------------------------------------------------------------

References

1
K. Ruedenberg, Rev. Mod. Phys., 1962, 34, 326.
2
R. F. W. Bader and M. E. Stephens, J. Am. Chem. Soc., 1975, 97, 7391.
3
R. L. Fulton, J. Phys. Chem., 1993, 97, 7516.
4
J. G. ngyn, M. Loos, and I. Mayer, J. Phys. Chem., 1994, 98, 5244.
5
X. Fradera, M. A. Austen, and R. F. W. Bader, J. Phys. Chem. A, 1999, 103,
304.
6
R. F. W. Bader, 'Atoms in Molecules: A Quantum Theory', Clarendon, 1990.
7
I. Mayer, Chem. Phys. Lett., 1983, 97, 270.
8
K. B. Wiberg, Tetrahedron, 1968, 24, 1083.
9
R. S. Mulliken, J. Chem. Phys., 1955, 23, 1833.
10
F. W. Biegler-Knig, R. F. W. Bader, and T.-H. Tang, J. Comput. Chem., 1982,
3, 317.
11
I. Mayer and P. Salvador, in 'Program 'FUZZY'. Available from
<http://occam.chemres.hu/programs>', Girona, 2003.
12
E. Matito, J. Poater, M. Sol, M. Duran, and P. Salvador, J. Phys. Chem. A,
2005, 109, 9904.
13
M. Gell, E. Matito, J. M. Luis, J. Poater, and M. Sol, J. Phys. Chem. A, 2006,
(submitted).
14
E. Matito, M. Sol, P. Salvador, and M. Duran, Faraday Discussions, 2006,
(accepted).
15
J. Poater, X. Fradera, M. Duran, and M. Sol, Chem. Eur. J., 2003, 9, 400.
16
J. Poater, X. Fradera, M. Duran, and M. Sol, Chem. Eur. J., 2003, 9, 1113.
17
E. Matito, M. Duran, and M. Sol, J. Chem. Phys., 2005, 122, 014109.
18
E. Matito, P. Salvador, M. Duran, and M. Sol, J. Phys. Chem. A, 2006, 110,
5108.
19
J. Poater, M. Duran, M. Sol, and B. Silvi, Chem. Rev., 2005, 105, 3911.