Dear Karolina Kula ,

These kind of images are very easy to obtain via the use of Gaussian. For this purpose, you should indicate the program to generate the *.chk file with the following command at the beginning of your input file: %chk=my_molecule.chk.

When your calculation is terminated you should see in the folder in which you made the calculation the file "my_molecule.chk".

You then use the Gaussian command "formchk": formchk my_molecule.chk

You obtain a new file called my_molecule.fchk

From this file you can easily obtain the first image with Gaussian using the two following command:

cubegen 0 density=SCF my_molecule.fchk my_molecule-dens.cube

(=> Generating the file my_molecule-dens.cube containing the information of the electron density of your molecule).

cubegen 0 potential=SCF my_molecule.fchk my_molecule-pot.cube

(=> Generating the file my_molecule-dens.cube containing the information of the electrostatic potential of your molecule).

It has to be noted you have different option for "density" and potential" like "MP2", "CC" or "CI" depending on the type of calculation you made (information can be retrieved from https://gaussian.com/cubegen/)

You can then used VMD to plot the first image with the following procedure I detailed in another discussion (https://www.researchgate.net/post/Displaying_electrostatic_potential_surface_in_Avogadro):

1. In "Main Window" : file > new molecule.

2. In "Molecule File Browser" just opened, "Browse" to find ****-dens.cube.

3. In "Main Window" : Graphics > Representations. In "graphical Representations" opened window you can click on "Drawing Method" and you choose your representation. you can do just whatever you want like "CPK", "Lines" etc... And adjust as you want "sphere scale", "bond radius" etc ...

4. To change colors as you desire : In "Main Window" > "Graphics" > "Colors". In "Colors Controls" opened window you can choose whatever you want. In "Color Scale" bar, you can choose a "Method". For your purpose maybe : "RGB".

5. In "Graphical Representations" window, you can click on "Create Rep": that just clones your representation. Then in "Drawing Method" you choose "Isosurface". You can adjust the "Isovalue" for example 0.001 for having and isosurface of electron density corresponding to Van der Waals surface. You can choose in "Material bar" > "Transparent" or "EdgyGlass" to have a transparent isosurface.

6. In "VMD Main" Window, just right click on the molecule you loaded and then "Load data into molecule". Choose you ****-pot.cube.

7. In "Graphical Representations" just do "Coloring Method" and then "Volume". In the little bar appearing just at right and in front of "Material" bar, choose your ***-pot.cube (by default it will choose ****-dens.cube).

8. Always in "Graphical Representations", you have bars like "Draw style", "Selections", "Trajectory" and "Periodic". Choose "Trajectory"

9. In "Color Scale Data Range" just choose negative and positive value to see appearing you potential electrostatic coloring on the isosurface.

10. When it is okay for you, you can export to an image. Usually I do "File" in "VMD Main" Window and then "render". In the just appeared "File Render Controls" I choose "Tachyon" in "Render the current scene using:" and in the "Render Command" I add just after "%s" the option "-res 1000 1000" you can put the dimensions you want. As well you will have "%s -res 1000 1000 -format TARGA -o ....". And "Start Rendering". You will have your graphical !

Nevertheless, I think you cannot obtain the ALIE function with Gaussian. For this purpose, the use of Multiwfn is recommended (http://sobereva.com/multiwfn/download.html). After downloading it, you can charge your *.fchk file in Multiwfn and follow the given procedure:

-> 5 Output and plot specific property within a spatial region (calc. grid data)

-> 1 Electron density

-> 3 High quality grid , covering whole system, about 1728000 points in total

-> 2 Export data to a Gaussian-type cube file in current folder

=> And you have your density.cub file generated.

The same procedure can be repeated changing the option of the second arrow with:

-> 12 Total electrostatic potential (ESP) (to have your electrostatic potential)

-> 18 Average local ionization energy (ALIE) (to have your ALIE function).

=> Your will generate two other cube files containing the information you need. You then can use VMD to obtain your desired image!

I also add an useful ability of Multiwfn to know exactly the scale of your ESP or ALIE function on a given isovalue of electron density:

-> Charge your *.fchk file in Multiwfn.

-> 12 Quantitative analysis of molecular surface

-> 1 Select the way to define surface, current: Electron density, iso: 0.00100 (no need to change if this is the isovalue of electron density you want)

-> 1 Electrostatic potential (ESP) (or 2 Average local ionization energy (ALIE))

-> 0 Start analysis now!

=> For ESP, you should give the path of Gaussian in the "settings.ini" file given with Multiwfn software.

-> 1 Export surface extrema as plain text file (if you want to export and keep a *.txt file containing the extrema of the function (ESP, ALIE etc ...)).

=> The most important minimum and maximum are indicated with a little "*". That gives you the scale to color your isosurface in the "Trajectory" of VMD!

Hope my answer could help you!

Please follow these video tutorials, which employ freely available Multiwfn (http://sobereva.com/multiwfn) in combination with VMD (http://www.ks.uiuc.edu/Research/vmd/) to plot the maps. More details can be found in Multiwfn manual.

Using Multiwfn and VMD to easily plot electrostatic potential colored molecular vdW surface map

https://youtu.be/QFpDf_GimA0

Using Multiwfn and VMD to plot average local ionization energy colored molecular surface map

https://youtu.be/-1sBa0lKhp8

Corentin Lefebvre thank you so much for comprehensive tutorial. I hope that I prepare the visualisation and data correctly.

Tian Lu thank you so much for your answer. I used multivin program several times in past and I know the sobereva channel very well (the YT channel is fantastic!). Thanks again.