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标题: Electronstatic potential for binding site [打印本页]

作者
Author: moiumuio 时间: 2024-4-15 00:06
标题: Electronstatic potential for binding site
Hi everyone,
I tend to use electrostatic potential topology analysis to study binding site between nitro group (-NO2) and my polymers. Is that an effective way to solve my issue? If not, can you suggest any better approaches?
thank you

作者
Author: sobereva 时间: 2024-4-15 04:28
If you view -NO2 as nucleophilic site, usually you just need to plot ESP colored molecular surface for polymer to check where its ESP is very positive, see Section 4.A.13 of Multiwfn manual on how to do. Using ESP topology analysis is deprecated, it is much more expensive while not quite intuitive.

However, it also should be noted that if the binding is not dominated by electrostatic interaction, van der Waals potential (J. Mol. Model., 26, 315 (2020)) should also be taken into account, see Section 3.23.7 and 4.20.6 of Multiwfn manual.

作者
Author: moiumuio 时间: 2024-4-16 19:56
本帖最后由 moiumuio 于 2024-4-16 20:06 编辑

sobereva 发表于 2024-4-15 04:28
If you view -NO2 as nucleophilic site, usually you just need to plot ESP colored molecular surface f ...

One more thing I want to know about this professor:.
Once I find the right binding site for my polymers, I want to check if there is electron (charge) transfer from them to a molecule that contains NO2 in an excited state (or during relaxation). Would FMO analysis be able to solve my issues, or do I need other methods?

作者
Author: sobereva 时间: 2024-4-17 04:31

moiumuio 发表于 2024-4-16 19:56
One more thing I want to know about this professor:.
Once I find the right binding site for my po ...

Calculating fragment charge for the molecule.
If the molecule is originally neutral, while its fragment charge is calculated to be e.g. -0.15 in a certain chemical environment, that means the molecule received 0.15 electron from other parts of the system due to charge transfer effect.

作者
Author: moiumuio 时间: 2024-4-17 10:25

sobereva 发表于 2024-4-17 04:31
Calculating fragment charge for the molecule.
If the molecule is originally neutral, while its fr ...

Is the effect of photoinduced electron transfer (PET), resonance energy transfer (RET), and dexter electron transfer explained by the fragment charge while in an excited state?

作者
Author: sobereva 时间: 2024-4-18 07:05

moiumuio 发表于 2024-4-17 10:25
Is the effect of photoinduced electron transfer (PET), resonance energy transfer (RET), and dexter ...

PET and DET can be discussed by fragment charge.

作者
Author: moiumuio 时间: 2024-4-18 13:10

sobereva 发表于 2024-4-18 07:05
PET and DET can be discussed by fragment charge.

In order to examine fragment charge, do I have to use #td opt?

作者
Author: sobereva 时间: 2024-4-19 05:23

moiumuio 发表于 2024-4-18 13:10
In order to examine fragment charge, do I have to use #td opt?

opt is not directly relevant
"density" keyword is needed, otherwise wavefunction will not be generated for excited state

作者
Author: moiumuio 时间: 2024-4-20 00:22

sobereva 发表于 2024-4-19 05:23
opt is not directly relevant
"density" keyword is needed, otherwise wavefunction will not be gene ...

I have followed this procedure
(1)# opt freq b3lyp/6-311G(d,p) geom=connectivity em=gd3bj
(2)# td cam-b3lyp/6-311G(d,p) density
Then the output of (1) and (2) will follow your guide: https://www.youtube.com/watch?v=xKvOLFbeGoc
If the acceptor of (2) has a greater negative charge than (1), a PET or DET would occur.
Am I okay with it?
Beside, can fragment charge could distinguish DET and PET? and are these methods "https://doi.org/10.1021/acs.jpcc.0c06694" "https://doi.org/10.1021/acs.jpca.5b01124" practical ?

作者
Author: sobereva 时间: 2024-4-20 08:02

moiumuio 发表于 2024-4-20 00:22
I have followed this procedure
(1)# opt freq b3lyp/6-311G(d,p) geom=connectivity em=gd3bj
(2)# ...

If you change the B3LYP in (1) to CAM-B3LYP, then it is correct.
I would like to also suggest performing hole-electron analysis using Multiwfn, which is much more intuitive, see Section 4.18.1 of Multiwfn manual on how to do.

I don't know how to distinguish them

作者
Author: moiumuio 时间: 2024-4-20 12:23
本帖最后由 moiumuio 于 2024-4-20 12:26 编辑

sobereva 发表于 2024-4-20 08:02
If you change the B3LYP in (1) to CAM-B3LYP, then it is correct.
I would like to also suggest per ...

CAM-B3LYP and B3LYP: which is better? I mean, in general, CAM-B3LYP is better for conjugated polymers, but some articles claimed the opposite, which is quite confusing.

作者
Author: sobereva 时间: 2024-4-21 04:52

moiumuio 发表于 2024-4-20 12:23
CAM-B3LYP and B3LYP: which is better? I mean, in general, CAM-B3LYP is better for conjugated polym ...

This depends on your specific purpose.
For calculating charge-transfer excited state, it widely known that CAM-B3LYP perform much better, while B3LYP tends to underestimate excitation energy. Because you need to obtain variation of fragment charge between ground state and excited state, and fragment charge of excited state is calculated using CAM-B3LYP, evidently that of ground state must also be calculated using this functional.

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