How to use EDDB Sílvia Escayola Gordils

07/19/2022

EDDB command-line options:

-a To diagonalize atomic blocks of the EDDB density matrix set it TRUE

-b To perform the EDDB analysis only for formally bonded atoms set it TRUE

-c To skip the EDDB calculations and perform the NPA analysis set it TRUE

-d Dissection [followed by the list of NOBD (natural orbitals for bond delocalization) to be
considered, e.g. 1:4] to compute the contribution of a particular orbital(s)

-e Molecular fragment (including non-local effects) [it is required to define the fragment, e.g.
1:4,7,8] select the EDDB_E function

-f Molecular fragment (excluding non-local effects) [it is required to define the fragment, e.g.
1:4,7,8] select the EDDB_F function. Takes into account the cross-ring delocalization effects

-g Select the EDDB_G (global) function. Delocalized bonds taking into account all atoms

-h Select the EDDB_H (no hydrogen atoms) function. Delocalized bonds excluding density of H
atoms

-i [e.g. MOLECULE.FCHK DMNAO.49] select input files

-m To reduce the full basis into the natural minimum basis (NMB) set it TRUE

-o Get the output for visualization of EDDB surfaces [e.g. EDDB_X.fchk] export the calculated
EDDB_X into a new .fchk file

-oo To visualize alpha and beta components of the EDDB(r) function set it TRUE

-p [delocalization pathway, e.g. 1-2-3-4-5-6-1] select the EDDB_P function. This function does not
take into account the cross-ring delocalization effects.

-q Disable interactive mode

-s To remove the UHF spin contamination and perform the EDDB analysis for paired (closed
subshell) and unpaired electrons (open subshell) set it TRUE

Common citations when using EDDB:

Szczepanik, D. W.; Andrzejak, M.; Dominikowska, J.; Pawełek, B.; Krygowski, T. M.; Szatylowicz, H.;
Solà, M. Phys. Chem. Chem. Phys., 2017, 19, 28970-28981.

Szczepanik, D. W.; Andrzejak, M.; Dyduch, K.; Zak, E. J.; Makowski, M.; G. Mazur, Mrozek, J., Phys.
Chem. Chem. Phys., 2014, 16, 20514−20523.

Szczepanik, D.W. RunEDDB (version 18-Jul-2022), http://aromaticity.eu (check if a newer version is

available at the time you use it. The script code is under active development so please check for
updates regularly ( runeddb -u ))
How to use EDDB Sílvia Escayola Gordils
07/19/2022

Examples:

Benzene S0 at CAM-B3LYP/6-311+g(d,p) level of theory.

Gaussian input to obtain mol.fchk and mol.49 files required for EDDB calculation:
%nproc=4

%mem=8000MB

%chk=mol.chk

#P CAM-B3LYP/6-311+g(d,p) gfinput density=current pop=nbo6read

mol

01

C -1.388894 -0.000000 0.000000

C -0.694447 -1.202818 -0.000000

C -0.694447 1.202818 0.000000

H -1.236256 -2.141258 -0.000000

H -1.236256 2.141258 0.000000

C 0.694447 -1.202818 -0.000000

C 0.694447 1.202818 0.000000

H 1.236256 -2.141258 -0.000000

H 1.236256 2.141258 0.000000

C 1.388894 0.000000 -0.000000

H 2.472511 0.000000 0.000000

H -2.472511 -0.000000 0.000000

How to use EDDB Sílvia Escayola Gordils
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$NBO SKIPBO FILE=mol DMNAO=W49 AONAO=W49 $END

*Calculations can also be performed with NBO3 version (default in Gaussian) replacing the
pop=nbo6read keyword by pop=nboread.
How to use EDDB Sílvia Escayola Gordils
07/19/2022

EDDB calculations:

RunEDDB -q -i mol.fchk mol.49 -g -o EDDB_g.fchk > EDDB_g.out

RunEDDB -q -i mol.fchk mol.49 -h -o EDDB_h.fchk > EDDB_h.out

The difference between EDDBG(r) and EDDBH(r) can be very useful in the identification of
multivalent hydrogen interactions. The net effect of 6 C-H bonds in benzene on electron
delocalization is 6.13e – 5.57e = 0.56e, which means that less than 0.1e shared between C and H
atoms is delocalized due to conjugation with other σ bonds in the system.

Each of the EDDB(r) functions can easily be dissected into σ-, π-, and higher symmetry
components. To do so, one has to check and select the natural orbitals for bond delocalization
(NOBD). The NOBDs are ordered from the high occupied to the low-occupied ones. One can
inspect the shape of the orbitals by visualizing the resulting EDDB_h.fchk file with Avogadro.
How to use EDDB Sílvia Escayola Gordils
07/19/2022

Since the NOBDs responsible for aromaticity usually have occupation numbers by an order of
magnitude greater than the rest of the orbitals, the symmetry dissection of EDDB is
straightforward (it is clear that orbitals 1-3 correspond to the π orbitals in benzene). For instance,
diagonalization of the EDDBH density matrix in benzene gives rise to 3 NOBDs (no. 1–3) with
occupation numbers from 1.7769e to 1.17756e and NOBDs (no. 4–21) with occupation numbers
from 0.0408e to 0.0010e. By summation of the corresponding NOBD occupation numbers, one
gets the following: π-EDDBH = 5.33e and σ-EDDBH = 0.24e; thus, even though the σ-delocalization
effects are still noticeable, benzene is clearly π-aromatic.

It may not be very useful for this particular case, since one can easily obtain the σ and π
contributions by the simple summation of occupation numbers (as shown above) but for more
complicated systems one may prefer to use EDDB to perform this calculation by selecting the
particular contribution of certain NOBDs.

RunEDDB -q -i mol.fchk mol.49 -h -d 1:3 -o EDDB_h_pi.fchk > EDDB_h_pi.out

How to use EDDB Sílvia Escayola Gordils
07/19/2022

Finally, one has EDDBF(r) and EDDBP(r) functions that can be used as local aromaticity measures. In
the case of EDDBF(r) all possible atomic pairs in the selected molecular fragment (usually cyclic unit
without H atoms) are considered. For benzene (or any other monocyclic molecule), this is
equivalent to the EDDBH(r) function, but it may not be the case in systems with more than one
ring.

RunEDDB -q -i mol.fchk mol.49 -f 1,2,6,10,7,3 -o EDDB_f.fchk > EDDB_f.out

One can also measure the delocalization of the fragment containing only the H atoms to realize
that there is no delocalization in this case (what a surprise!).

RunEDDB -q -i mol.fchk mol.49 -f 4,5,8,9,11,12 -o EDDB_f_H.fchk > EDDB_f_H.out

The situation is slightly different with the local EDDB P(r) function, which “measures” electron
delocalization along the selected pathway of adjacent bonds (only takes into account Kekulé
How to use EDDB Sílvia Escayola Gordils
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structures, while EDDBF takes into account, Kekulé, Dewar, and all the other possible cross-ring
delocalization effects).

RunEDDB -q -i mol.fchk mol.49 -p 1-2-6-10-7-3-1 -o EDDB_p.fchk > EDDB_p.out

EDDB allows for the visualization of the delocalized density of any of the EDDB functions
computed. To generate the plot one has to open the resulting .fchk file with Avogadro, go to
Extensions > Create Surfaces, select surface type and color by “electron density”, and set the iso
value and resolution to the desired values > calculate.

Alternatively, the cubgen functionality of Gaussian can be used to obtain a cube file that can be
read by many visualization programs.

cubegen 2 FDensity=SCF name_file.fchk name_file.cube

Benzene T1 at CAM-B3LYP/6-311+g(d,p) level of theory (using S0 optimized geometry).

You run the program the same as for a closed shell, but you get alpha/beta separation in the
output.
How to use EDDB Sílvia Escayola Gordils
07/19/2022