NBO View

The NBO view program is used to create 1D,2D and 3D images of the orbitals
which have been calculated using the NBO program.
The NBO view program is installed in the ubuntu operating system. The NBO
program creates files of the type FILE.31, FILE.32,. . . , which will be used for NBO
view.

1 2D contour plots
The 2D contour plots are first plotted to visualize the orbital amplitude (or electron
density) in a chosen plane within the molecule, which will also help in visualizing
orbital overlap.
Steps to be followed:
1. Open terminal on ubuntu 1 and go to the folder containing the NBO files for
the molecule FILE.31, FILE.32,. . . , using the cd command on the terminal.

2. Enter the command nbov which will start the NBO View program on the
terminal. Then press Enter to continue.

3. The program asks Input filename for this job to which type in FILE(all
caps) and press Enter. Then press enter when the program asks are these
entries OK.

4. The NBO view command page opens subsequently and command: prompt
is seen.

5. Type basis pnbo after the command: prompt, and press enter.

6. Open the output file generated after NBO analysis and look for the required in-
teraction. Note down the atom ID numbers of the atoms involved in interaction
as well as the serial number of the donor and acceptor NBO.
1
> icon in the taskbar

1
 7. Then type plane in the command: prompt of the terminal and press enter.
This command is used for specifying the plane containing the atoms in the
molecule whose contour plot is to be drawn.
The Definition of Plane window appears:

Enter three atom numbers: Enter the IDs of the three atoms which were
noted down previously.
Press Enter three times.
Enter minimum and maximum X values : type -5 5 and press enter.
Enter minimum and maximum Y values : type -5 5 and press enter.
Press enter twice.

8. The command prompt reappears.

Type contour (serial number of the NBO)2 .
An image of the contour plot appears on the screen. Press enter. This will be
stored in the storage location as indicated in the bottom right corner of the
terminal screen. Note down the storage location number.

9. To create the image file of conotour plot:

Type draw (storage location number of the contour plot).
For eg. draw 1 or draw 1 2.
Hardcopy options will be displayed. In the Your choice type 43 .
In [Desired file name]: type the name you want to give to the file. Press enter
four times. The contour plot would have appeared in your folder.

10. Similarly produce the contour plot(s) of the other orbital(s) whose orbital over-
lap has to be shown.

11. If the solid lines of the orbitals are not overlapping in the contour plot then
change the sign of one of the orbital. For this type sign - in the command
prompt. Then again make the contour plot for that orbital using contour
command.

2
type only the serial number without the brackets
3
Choice 4 is for .bmp image file.

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2 3D rendered images
To create 3D images showing the orbital overlap, the steps to be followed:

1. Type view (storage locations number of the NBOs)

For eg. view 1 2.
If you are giving the view command for the first time, camera options will be
displayed:

(a) In the camera and light source parameters type n(no) for Are these
values OK ([Y]/N).
Camera distance from screen : Set it to 14. You can change it as you
see fit, to zoom in or zoom out.
two rotation angles (about X,Y) : Altering these angles gives the effect
of rotating the molecule about a horizontal or vertical axis. The input
rotation angles will be treated as the change with respect to a previous
camera orientation, making it easy to pan around the viewed object.
Press enter four times.
(b) Colour (blue/green/red) properties :
Set the background colour to 1 1 1 to obtain white background. By
default it is set to blue.

2. Press enter for all the parameters that follow till Bitmap filename [ ]: appears.
Here enter a name for the 3D image file and press enter. Wait till the image is
created in the folder.

3. If the camera angle of the 3D image created is not satisfactory change the
camera angle using the command camera in the command prompt.

Additionally, guidelines for the NBO View software with detailed description of
all the commands used can be found in this link :
http://nbo6.chem.wisc.edu/v_manual.htm