Suppose you want to get nice molecular orbital renderings for your paper or a blog post. Let’s do it using gOpenMol. It is an old program, developed by Leif Laaksonen. It was available at the web-site of IT CENTER FOR SCIENCE earlier, but only a manual is still there. I managed to download the program itself from Softpedia, and tested it uder Win7. As gOpenMol is an old piece of software, you will need a .fchk file made by Gaussian03. I tried to use G09-generated files, but the program crashes.
- Prepare .fchk file. You will get a .chk file after a Gaussian calculation. Then perform a following command:
2. Launch gOpenMol and open
Tools > Plugins > FCHK Handling. Press
Browse in the opened window, select your .fchk file and press
Load. You will get something like this:
3. Set all
Grid parameters to 60 (for smoother surfaces). Press
4. Select option
Use selected orbital and choose needed orbital. Filled MOs are denoted by asterisk in the list and ordered by energy ascending. Then press
Calculate Grid. You will need to repeat this part as many times as the number of orbitals you want to render.
5. Close the window by pressing
6. Change the background color to white.
View > Background color > Color. Choose white and press
7. Change the rendering style to balls&sticks.
View > Atom type. Select
Licorice in the opened window. Change the thickness of bond cylinders to 0.15 in the
Cyl.rad field. Press
Apply and close the window.
8. Let’s show the orbitals, finally!
Plot > Contour will open the following window:
Orbitals with the grids calculated at step 4 will appear in the upper list. Choose one of them.
9. Put two thresholds in the first and second rows of the field named
Define contour levels. In my case 0.04 and -0.04 were good.
10. Select colors for the positive and negative regions. I prefer dark blue and gray.
11. Press apply.
12. It’s not over yet! Press green
Details... button next to the field with entered threshold and put the settings in the window that appears as follows:
13. After all the settings are done, press
Apply and close the window. Do the same for the second threshold value in the
Define contour levels field.
14. Almost ready. Rotate and zoom your molecule as you like. 3D rotation is done with the left mouse button pressed, the right mouse button is for zooming, and for 2D rotation you need to keep the mouse wheel pressed. Final image size will correspond to the window size, so it’s better to make your molecule as big as you can. Use
Edit > Rotate/Translate to place the molecule at the center and to translate it.
15. Save the image by choosing
File > Hardcopy… Select BMP, enter the file name and location using
Browse button and save the image by pressing
I have translated this guide from my old post in Russian at chemport.ru website. This way of preparation orbital images was used in our paper Kirilchuk, A. A.; Rozhenko, A. B.; Leszczynski, J. On Structure and Stability of Pyrimidine Ylidenes and Their Homologues. Comput. Theor. Chem. 2017, 1103, 83–91.