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Ossama

Member

Registered: 2019-11-12

Posts: 20

Vomume enclosed by a function isosurface

Hi
Thank you for your effort. I am really impressed.

I've a question regarding defining an isosurface of the molecule in Multiwfn, in particular, the area of the surface or the volume enclosed by it.

In "Quantitative analysis of molecular sufrace",  If I choose, say, electron localization function, and I set the subsurface value to be 0.7. Here I will have many isosurfaces that enclose many volumes. Then, the values of area and volume I get from Multiwfn, are they supposed to be the sum of all obtained isosurfaces' areas and volumes?

Besides, if I choose the isosurface value to be, say, 0.1. Here, I am supposed to have an isosurface that encloses other isosurfaces. Then, do the values obtained for the molecular surface and the volume enclosed represent the outer isosurface only?

Thanks!

Last edited by Ossama (2020-05-17 23:39:04)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: Vomume enclosed by a function isosurface

The surface area and volume in main function 12 are reported for all isosurfaces. If you need to obtain area and volume for individual isosurface, the most convenient way is exporting the grid data as cube file, and then use ChimeraX to examine character of specific isosurface. See 4:27 of this video tutorial:
Plotting electron localization function (ELF) isosurface using Multiwfn and ChimeraX
https://youtu.be/vC48iEB8PwI

Regarding the second question, it is better to upload an image, otherwise I am unable to clearly understand your representation.

Ossama

Member

Registered: 2019-11-12

Posts: 20

Re: Vomume enclosed by a function isosurface

Regarding the second question, it is better to upload an image, otherwise I am unable to clearly understand your representation.

This is an ELF representation of FI molecule. The isosurface value is 0.2.

According to the ELF there are one (or more than one) isosurface that is contained in another isosurface. Here isosurface 2 encompasses isosurface 1, albeit being with the same value. 

So when I am given the isosurface characteristics by Multiwfn like area, volume etc, does it mean the outer surface only or all the surfaces?

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: Vomume enclosed by a function isosurface

I use 2D map to represent your situation more clearly

The volume reported by Multiwfn corresponds to the sum of the two blue regions, the surface area reported by corresponds to all the three red lines.

Ossama

Member

Registered: 2019-11-12

Posts: 20

Re: Vomume enclosed by a function isosurface

What if I need to study the outer surface separately, its area, the volume which it encloses (all the enclosed volume), mapping it with electron density or electrostatic potential and finding out the areas of positive and negative electrostatic potential etc? Is it possible with Multiwfn? If I use Chimera, do I get what I need?

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,622

Website

Re: Vomume enclosed by a function isosurface

To obtain surface area and volume in the outer shell, use ChimeraX is the most convenient way.
Mapping ESP to ELF isosurface is usually nonsense, no data of chemical interest can be obtained.
Mapping electron density to ELF is also not useful, I cannot imagine which chemically meaningful information could be extracted from this kind of analysis.

If you indeed need to map specific function on the valence ELF isosurface, you can consider to use pseudopotential for the atom, then the core ELF isosurface will disappear.