John Keller University of Alaska Fairbanks

Example dipole and dipole+ESP surface display for S-Chlorofluoroaminomethane

Electron density: 0.020 e/bohr3 ;  Electrostatic potential scale: -0.15 to 0.07 e/bohr . (B3LYP/6-31G(d,p))

This example uses the output.log from an ORCA optimization job

Input.inp:

! B3LYP 6-31G(d,p)
! OPT
* xyz 0 1
C 0.00000000 0.00000000 0.00000000
N 1.40635900 0.00444500 -0.02777100
H 1.77564700 0.95076400 -0.01696900
H 1.78236900 -0.51878400 0.75806500
F -0.54662700 0.66115000 1.08564100
H -0.39093600 -1.01869200 -0.00145500
Cl -0.64682900 0.82084200 -1.48130100
*

Step-by-step using Jmol.

In WebMO, export the structure as fclma.mol; export the electron density surface as fclma-dens.cub; export the electrostatic potential as fclma-esp.cub.

fclma.mol    fclma-dens.cub    fclma-esp.cub
 

In WebMO the dipole moment is shown at the cartesian center, and is about 2.5x the length of the dipole given in the  "Dipole Moment" table at the end of the ORCA output.log file.

For a given molecule, the dipole coordinates can be calculated from the dipole given in the ORCA table using a spreadsheet. For this case, the spreadsheet is here.

(ORCA gives the dipole direction as defined by physicists. As chemists, we therefore take the negative of the initial dipole coordinates in output.log.) The ORCA dipole also originates at the cartesian origin (0,0,0), so this must be moved to the "WebMO" location in the spreadsheet. The spreadsheet creates a Jmol "dipole" command using the calculated dipole coordinates, which can then be pasted into the Jmol console (it has already been done in this example).

For your molecule, the (negative of the) dipole coordinates from the ORCA table should be entered in Row 3. The cartesian coordinates of the molecule are entered beginning at Row 18. The cartesian coordinates of the molecule can be obtained from the ORCA "CARTESIAN COORDINATES (ANGSTROEM)" table, or exported in XYZ format from WebMO.

Using Jmol, the set of commands with comments are as follows:

cd <directory containing 3 files>
load fclma.mol;
background white;
set antialiasdisplay on;
color bonds gainsboro;
zoom 100;
dipole dip width 0.2 {1.3625 -0.3475 0.818} { -0.2625 0.6275 -0.632};  // dipole like WebMO
color dipole blue;                                                    
// dipole dip width 0.2 {3.15 -1.42 2.413} { -2.05 1.7 -2.227};        // 8x dipole
// color dipole yellow;
isosurface esp cutoff 0.02 fclma-dens.cub color absolute -0.18 0.07 fclma-esp.cub;
isosurface esp translucent 99;
isosurface fullylit;
 isosurface off;
// isosurface on;