Dariusz W. Szczepanik1,2

1  Department of Theoretical Chemistry, Jagiellonian University
    Faculty of Chemistry, Gronostajowa 2, 30-387 Krakow, Poland
2  Institute of Computational Chemistry and Catalysis, University of Girona
    C/ Maria Aurèlia Capmany, 69, 17003 Girona, Catalonia, Spain

PL  Input files

The current version of RunEDDB requires two input files: the formatted checkpoint file (.fchk) and DMNAO.49 file. The latter can be generated using the NBO program by specifying $NBO SKIPBO FILE=DMNAO AONAO=W49 DMNAO=W49 $END. If you use Gaussian (09 and later) and already have an unformatted checkpoint file from previous HF/DFT calculations, MOLECULE.CHK, you can generate DMNAO.49 using the following Gaussian input file:

It is strongly recommended to install and use the newest NBO7 module (keyword POP(NBO7READ,NONE) in the Gaussian route section), especially when diffuse functions are used (in this case adding IOP(3/32=2) in the Gaussian route section is also recommended).

PL  Important parameters and command-line options:

PL  Types of the EDDB(r) function

  1. EDDBG  -  electrons delocalized through the system of all chemical bonds in a molecule (Global delocalization).
  2. EDDBH  -  electrons delocalized through the system of all chemical bonds involving only Heavy atoms.
    To study global π-delocalization it is recommended to use this function rather than EDDBG because the bond orbitals involving hydrogen atoms tend to conjugate with the adjacent σ-bond orbitals noticeably increasing delocalization in the σ-subsystem; both funtions give almost quantitatively the same predictions of π-delocalization if manual dissection of NOBDs of π-symmetry is performed (option -d).
  3. EDDBF  -  electrons delocalized through the system of chemical bonds in particular molecular Fragment.
  4. EDDBE  -  similar to EDDBF, but here the density of electrons delocalized in selected fragment is "extracted" (cut down) from the EDDBG function, and thus it includes also the External (non-local) resonance effects.
  5. EDDBP  -  electrons delocalized along selected Pathway.

PL  Visualization of EDDB and its eigenfunctions (NOBDs)

To visualize the EDDB(r) function set  SAVE_EDDB_TO_GAUSSIAN_FCHK = TRUE  or use command-line option  -o . The created new checkpoint file, e.g. EDDB_G.fchk, is a copy of the original (input) one in which Alpha MO energies and coefficients as well as the Total SCF density (and Spin SCF density for open-shell systems) are replaced by the (spinless) Natural Orbital for Bond Delocalization (NOBD) occupation numbers, NOBD coefficients, and the total EDDB density (and spin EDDB density for open-shell systems), respectively. EDDB_G.fchk can be used to generate the cube file using cubegen program from the Gaussian package, e.g.:

 cubegen.exe 4 FDensity=SCF EDDB_G.fchk EDDB_G.cube 100 h

Alternatively one can use Avogadro to visualize the EDDB function. To do that open the EDDB_G.fchk and in the program menu select Extensions -> Create Surfaces -> Surface Type: "Electron Density", Iso Values: "0.020" and click the button. To visualize NOBDs, use the toolbar "Orbitals" on the right site of the program window (the toolbar can be turned on/off in the menu Settings -> Toolbars -> Orbitals). The NOBDs are ordered by decreasing occupation number; thus, e.g. in the case of π-aromatic systems the π-NOBDs are expected to be at the beginning of the list.




Last update:    2020-04-18