eddb.pl

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:

 
 %OLDCHK=MOLECULE.CHK
 %NOSAVE
 #T CHKBASIS GUESS(READ,ONLY) GEOM(ALLCHECKPOINT) POP(NBOREAD,NONE)
 
 $NBO SKIPBO FILE=DMNAO DMNAO=W49 AONAO=W49 $END
 
 
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