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Re: ESP area around selected point and maximum not equal

dummy@example.com (sobereva) — Wed, 19 Jul 2023 14:32:57 +0000

Temporarily I don't have a clear plan to make Multiwfn derive the parameters in Fig. 1. In fact they can be very easily measured in VMD program based on the surface vertices and surface extrema exported by Multiwfn.

Tian

Re: ESP area around selected point and maximum not equal

dummy@example.com (martinj) — Wed, 19 Jul 2023 09:32:43 +0000

Hi, thank you, that was exactly what I was looking for.

By the way, have you though about incorporating surface calculation as described in Fig. 1 by Kolar, et al. (https://doi.org/10.1039/C4CP02621G)? I would solve problems you described in section 4.12.10 (at least for sigma holes).

Re: ESP area around selected point and maximum not equal

dummy@example.com (sobereva) — Wed, 19 Jul 2023 02:38:00 +0000

Please check "(3) Analysis of local molecular surface based on Basin-like partition" in Section 3.15.2.2 of Multiwfn manual, there is a brief introduction of the basin-like surface analysis algorithm used in Multiwfn.

Tian

Re: ESP area around selected point and maximum not equal

dummy@example.com (martinj) — Tue, 18 Jul 2023 20:14:47 +0000

So, I checked the ESP surface and it seems it really is almost entirely positive near the Cl atom. I was wondering how exactly is the algorithm of calculation implemeted. If I use option 14, is there any limit to where does it consider the surface to correspond to the maximum? It appears for area corresponding to atom (as using option 11) there is a limit?

Re: ESP area around selected point and maximum not equal

dummy@example.com (martinj) — Tue, 18 Jul 2023 14:20:23 +0000

Hi again,
I tried option 14 and in general it worked well. However, in some cases, e.g. with another substituent present on the aromatic core, the positive area calculated by option 14 was huge, e.g. area around atom (option 11) is 20.46 and area around the maximum is 109.18. Any idea what could be the issue and how to approach it? Thank you for the help.

Re: ESP area around selected point and maximum not equal

dummy@example.com (sobereva) — Wed, 12 Jul 2023 02:10:18 +0000

Yes, option 14 aims for this purpose.

Re: ESP area around selected point and maximum not equal

dummy@example.com (martinj) — Tue, 11 Jul 2023 23:00:30 +0000

Dear Tian,

Thank you very much for the reply.

As the difference is not that big, I assumed there might be an algorithm difference, still, visual check of the ESP colored vdw surface is a good idea.

Based on what you wrote, if I wanted to get the positive area of the sigma hole, option 14 should be more precise then?

Thank you

Re: ESP area around selected point and maximum not equal

dummy@example.com (sobereva) — Tue, 11 Jul 2023 20:50:39 +0000

Dear Martin,

Perhaps not only the sigma-hole region, but also other regions on local vdW surface of Cl show positive ESP. I suggest carefully checking ESP colored vdW surface map.

In addition, the algorithm of determining the area is slightly different. Note that each surface triangle is composed of three surface vertices. In the case of option 11, a surface triangle is considered if function value at its center satisfies the threshold; however, in option 14, a surface triangle is considered only if function values at all its three vertices satisfy the threshold.

Best,

Tian

ESP area around selected point and maximum not equal

dummy@example.com (martinj) — Tue, 11 Jul 2023 10:00:50 +0000

Hi,
I noticed that when I do quantitative analysis of the molecular surface (option 12), the calculated area of positive ESP for selected atom is not equal to the area, when calculated around specific point (the point being maximum of ESP around the same atom).

E.g. for a Cl atom in my molecule, the positive ESP area calculated by option 11 is 2.00629A^2, but the area calculated by option 14 for the maximum of Cl atom, defined as >0 (last input using option 14), is only 1.726A^2.

Could you assist me with this? Which value should be taken?

Thank you.

Martin