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标题: What is a pseudoradical and pseudodiradical speces ? [打印本页]
作者Author: zako 时间: 2021-10-21 03:18
标题: What is a pseudoradical and pseudodiradical speces ?
Hello everybody,
Three-atom-components (TACs) used in [3 +2] cycloaddition (32CA) reactions has been classified into four different structures Pseudodiradical, Pseudoradical, Carbenoid and Zwitterionic.
I searched for the definition of pseudoradical and pseudodiradical and i found some articls, but i still don't understand their meaning.
I hope that you clarify those terms ? and the most important thing how can i run a gaussian calculation on those two types of compound ?
Note: During my searching i found that diazomethane is a pseudoradical compound.
Many thanks in advaces
作者Author: sobereva 时间: 2021-10-21 04:24
Pseudodiradical shows certain degree of diradical character, but it is not a diradical in strict sense, namely its stable wavefunction is a closed-shell state. However, if you use Multiwfn code to perform ELF basin or topology analysis for the system in the pseudodiradical status, you will find in the region where new bond will form, some electrons already localized at the two respective atoms; in the language of ELF analysis, there are monosynaptic basins. See my paper RSC Adv., 2015, 5, 62248–62259 (DOI: 10.1039/c5ra08614k) for example. In the following figure from the paper, the IRC point P6 shows typical pseudodiradical character, as there are two monosynaptic basins between the carbon atoms about to form bonds (the purple spheres in the following figure correspond to the ELF attractors of the corresponding ELF basins).
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作者Author: zako 时间: 2021-10-21 06:39
本帖最后由 zako 于 2021-10-21 06:41 编辑
Thank you very much Professor, for the wonderful research piece, everything is clear now.But, in the case of diazomethane which is considered as pseudo-radical species, why there is two monosynaptic basin (black cercle)? And about the isosurfaces of electron localization function (ELF) of diazomethane, the two black squares that represent monosynaptic basin (red color), but when i did my own calculation with the same level of theory i found it green (disynaptic basin), why there is such difference?
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作者Author: sobereva 时间: 2021-10-21 06:52
zako 发表于 2021-10-21 06:39
Thank you very much Professor, for the wonderful research piece, everything is clear now.But, in the ...
The V(C1) and V'(C1) must be monosynaptic basins, because they correspond to the highly localized electrons at C1, rather than correspond to the electrons responsible for bonding between two atoms.
作者Author: zako 时间: 2021-10-21 07:24
Why i get a green color insted of red which is wrong ? I repeat the calculation many times, always the same results
作者Author: sobereva 时间: 2021-10-21 08:17
zako 发表于 2021-10-21 07:24
Why i get a green color insted of red which is wrong ? I repeat the calculation many times, always ...
Please upload your isosurface map, otherwise I cannot comment
作者Author: zako 时间: 2021-10-21 20:21
本帖最后由 zako 于 2021-10-21 20:30 编辑
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Multiwfn is very good in ELF analysis (fast and easy to use), but coloration isn't automatic like Topmod09 program. As the images show, if i change the isovalue i can't seperate the colors.
作者Author: zako 时间: 2021-10-21 22:53
I oploeded the isosurface maps as you requested, Multiwfn give the same results as topmod with less time and very handy to manipulate, but there is only one difference which a second cube file (esyn), that allow us to colorate different basin automatically. why there isn't the same process in Multiwfn ?
作者Author: sobereva 时间: 2021-10-22 02:56
Topmod doesn't have any ability to draw ELF map, the current map is plotted by Chimera or ChimeraX
You can use Multiwfn to export cube file of ELF, then visualize it in Chimera and properly color various isosurfaces according to basin types, see http://sobereva.com/168 and https://youtu.be/vC48iEB8PwI
Beware that it is dangerous to "automatically" identify type of ELF basins (monosynaptic or disynaptic), especially when the electronic and geometric structure is complicated. It is no perfect algorithm that able to gurantee that the basin type can always be correctly assigned. Rather than the risk of identifying the wrong basin type, I would rather let the user manually identify the type based on the image, after all it is very easy.
作者Author: zako 时间: 2021-10-22 03:11
Dear Professor,
The last two images, i plotted by me using chimera like you explained in your tutorial, what i want to say is that the coloration change according to isovalue, which is wrong, in contrary topmod generate two .cube files elf.cube and esyn.cube, the last cube file esyn.cube contain the color code, and by using pymol the coloration is automatic and doesn't change by changing the isovalue.
作者Author: sobereva 时间: 2021-10-22 03:19
zako 发表于 2021-10-22 03:11
Dear Professor,
The last two images, i plotted by me using chimera like you explained in your tut ...
Commonly, one should determine basin type based on attractor map according to relative position of attractors and atoms. Then, plot ELF isosurface map and gradually adjust the isovalue to a proper value, so that main characters of the basins of interest can be clearly visualized by current isosurface; finally, manually color the isosurfaces according to type of their corresponding basins.
作者Author: sobereva 时间: 2021-10-22 05:56
I just updated Multiwfn on Multiwfn website, now it is able to easily plot ELF isosurface map colored by basin type (monosynaptic, disynaptic and others) in VMD, the isosurface color will not change when isovalue changes, and a single isosurface can be colored differently in various subregions corresponding to different types of basins. see Section 4.17.10 of updated Multiwfn manual for example.
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作者Author: zako 时间: 2021-10-24 06:50
Dear Professor,
Thank you very very much.
作者Author: mekelleche 时间: 2021-11-15 23:07
本帖最后由 mekelleche 于 2021-11-17 05:26 编辑
Professor Sobereva,
The new feature in Multiwfn for coloring isosurfaces automatically is very good and wonderful, but there is one tiny detail annoying, which is that the core basin has the same color with the disynaptic basin V(C,H), is it possible to differentiate the colors of those two basins by giving them different colors ?Please, I hope you could update Multiwfn program to include the core basin.
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作者Author: sobereva 时间: 2021-11-17 14:09
I just updated Multiwfn 3.8(dev) on Multiwfn website, and updated example in Section 4.17.10 of Multiwfn manual. As you can see, via new option, now you can easily plot isosurfaces for selected basins and directly specify their color.
作者Author: mekelleche 时间: 2021-11-17 19:33
Dear Teacher,
Thank you very much for the update, and I just want to add a little tiny remark that in the new version of vmd 1.9.4, there is a new coloration scale based on four colors like plasma, viridis, the thing that will allow us to color each basin with it's own color, and I think it's better to differentiate between the two 2-synaptic basin V(atom,atom) and V(atom,H) by coloring it with two different colors.
Thank you very much once again
作者Author: sobereva 时间: 2021-11-18 04:53
I will consider this when formal version of VMD 1.9.4 is released. The current candidate version of VMD 1.9.4 has a lot of bugs and hence I never use it.
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