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laducaan

Member

Registered: 2025-11-29

Posts: 3

Generating electrostatic potential surface in specific volume

Hi,

I want to generate an electrostatic potential surface or (charge distribution) of a singular NO_{3} ligand in an octahedral Zn complex.
This is to compare it to a control ligand's NO3 ion, and free NO3.

Does anyone have any advice for generating this type plot with the volume surrounding just the NO3 ligand?

Cheers,

sobereva

Tian Lu (Multiwfn developer)

From: Athens, Greece

Registered: 2017-09-11

Posts: 2,154

Website

Re: Generating electrostatic potential surface in specific volume

I don't quite understand your question. But I would like to mention it is possible to obtain volume of a fragment (e.g. a ligand in coordinate) via AIM basin analysis. Please check Section 4.17.1 of Multiwfn manual, as you can see via basin analysis, one can obtain volume of each atom enclosed by 0.001 a.u. electron density isosurface.

laducaan

Member

Registered: 2025-11-29

Posts: 3

Re: Generating electrostatic potential surface in specific volume

Thank you for your prompt response.

I think what I want is the electrostatic potential mapped onto the molecular surface (i.e, the van der Waals surface). So i'd want to confine the grid generation to just the volume surrounding the NO3 ligand, and then map the overall electrostatic potential onto that as a coloring. I think if I have the cube set to the right grid volume around the nitrate, it should work.

I'm just unsure how to generate the VdW spheres for a specific volume.

I'm targetting these images, but not for my entire coordination complex, just the region surrounding a nitrate ligand. http://sobereva.com/multiwfn/res/plotESPsurf.pdf

Last edited by laducaan (2025-11-30 15:46:53)

laducaan

Member

Registered: 2025-11-29

Posts: 3

Re: Generating electrostatic potential surface in specific volume

To anyone else who wants to do something similar, plotting electrostatic potential over the electron density surface:

Take a molden, .wfn, or .fchk file, load, and use

5 Ouput and plot specific property within a spatial region (calc. grid data)
1 Electron density (rho)
11 Select a set of atoms, set extension distance around them and grid spacing

2.3 A around a central atom of the NO3 ligand worked well.

Density saved to a cube file as density.cub

Repeated with option 5 -> 12 Total electrostatic potential (ESP), saved as totesp.cub

Loaded density.cube into VMD, and totesp.cub isolated just the NO3 atoms I wanted, then colored the isosurface according to volume of totesp.cub.

Color scale set to RGB to have red be the negatively charged areas and blue be positive.