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Interpretation of Electron Spin Density lobes after doing DFT
darkdevil:
Hi!
I havn't been posting questions here for quite a while, hope everyone is safe in this pandemic :O
I was trained as an organic chemists and am still new to DFT using Gaussian.
I just did an open shell unrestricted DFT calculation of an organic radical cation (positively charged, doublet state) , and generated some really nice electron spin density pictures. What I am not sure about is the difference between the positive and negative ISO values of the lobes after generating the cube files. They turned out to be displayed as blue (positive) and green (negative) lobes wrapped around the molecule in GaussView. I am wondering what does the physical meaning of it?
Do the "balloons" mean where the extra "radical" electron will be most likely to locate? but why there are two different colors? I am guessing if blue represents the "up" spin state and green represents the "down" spin state?
Image is attached below:
Thanks and stay safe!
pm133:
It looks to me like you might have some spin contamination here. Your output file will tell you that.
The colours are for spin up and spin down.
If there's no spin contamination then this might be showing that your unpaired electrons are delocalised.
darkdevil:
--- Quote from: pm133 on May 12, 2020, 08:03:59 AM ---It looks to me like you might have some spin contamination here. Your output file will tell you that.
The colours are for spin up and spin down.
If there's no spin contamination then this might be showing that your unpaired electrons are delocalised.
--- End quote ---
Thanks for your reply.
What exactly is a spin contamination and how do you know there is such contamination by looking at the ESD images? and how do I check it in the output file? I googled about it and have a rough idea that it is related to a different in spin multiplicity than the input spin state, but what causes this to happen?
pm133:
Your question worries me slightly because it suggests you might be trying to use Gaussian as a black box tool. Is this the case? I'll assume for now that you know the maths behind this stuff and try to explain. If you don't know, you might need someone to help you.
Your spin state is not a pure doublet because in unrestricted shell calculations your determinants are not eigenfunctions of the S^2 operator.
Instead, it's an approximate doublet formed from a linear combination of doublet, quartet, sextet etc. spin states.
These higher spin states remain in the calculation and hence the name "spin contamination". As I remember, it forces a higher S^2 value than you would expect for a pure state and the energy increases as well.
Visually, you can get a clue to this potentially happening when you see your doublet smeared across a molecule when you don't expect it and specifically when you see phases of up and down spin split up and spread across the molecule as you see in your diagram.
Firstly, check your Gaussian output file to see the result of the calculation and make sure it is an unrestricted solution (which I'm sure it will be). It will tell you next to the final energy value.
Secondly there should be a value of S^2 alongside the result I think. That SHOULD be what you would expect for a pure doublet (0.7500) but it will be different and if I remember always higher than this because of the inclusion of higher spin states which you have not removed. I think Gaussian might try to use projection operators to remove as much of it as it can but I seem to remember this not being trivial at all and isn't guaranteed to work.
If you do have spin contamination you need to determine how bad it is by seeing how far from the pure doublet value you get. If it goes higher than 10% above this figure then you can't use the result because it's contaminated beyond repair. Either way, you need to check for wavefunction instabilities to check if a lower energy solution can be found. Use the Gaussian docs to see how to do that as I've been out the game for 3 years and I've forgotten. I think there's a keyword "...something...=stable".
My PhD was in open shell calculations using transition metals and I can assure you it isn't necessarily a trivial exercise to get to results you know you can trust. It's nice to see you being ambitious about using the tools but Gaussian isn't a block box for open shell stuff. You'll maybe need to start diving into the theoretical stuff as described in Szabo and Ostlund (Modern Quantum Chemistry). They do a great description of spin contamination on pages 104 to 107.
I'm afraid you've not asked a trivial question here so good luck with it. Let me know how you get on.
darkdevil:
--- Quote from: pm133 on May 12, 2020, 04:47:18 PM ---Your question worries me slightly because it suggests you might be trying to use Gaussian as a black box tool. Is this the case? I'll assume for now that you know the maths behind this stuff and try to explain. If you don't know, you might need someone to help you.
Your spin state is not a pure doublet because in unrestricted shell calculations your determinants are not eigenfunctions of the S^2 operator.
Instead, it's an approximate doublet formed from a linear combination of doublet, quartet, sextet etc. spin states.
These higher spin states remain in the calculation and hence the name "spin contamination". As I remember, it forces a higher S^2 value than you would expect for a pure state and the energy increases as well.
Visually, you can get a clue to this potentially happening when you see your doublet smeared across a molecule when you don't expect it and specifically when you see phases of up and down spin split up and spread across the molecule as you see in your diagram.
Firstly, check your Gaussian output file to see the result of the calculation and make sure it is an unrestricted solution (which I'm sure it will be). It will tell you next to the final energy value.
Secondly there should be a value of S^2 alongside the result I think. That SHOULD be what you would expect for a pure doublet (0.7500) but it will be different and if I remember always higher than this because of the inclusion of higher spin states which you have not removed. I think Gaussian might try to use projection operators to remove as much of it as it can but I seem to remember this not being trivial at all and isn't guaranteed to work.
If you do have spin contamination you need to determine how bad it is by seeing how far from the pure doublet value you get. If it goes higher than 10% above this figure then you can't use the result because it's contaminated beyond repair. Either way, you need to check for wavefunction instabilities to check if a lower energy solution can be found. Use the Gaussian docs to see how to do that as I've been out the game for 3 years and I've forgotten. I think there's a keyword "...something...=stable".
My PhD was in open shell calculations using transition metals and I can assure you it isn't necessarily a trivial exercise to get to results you know you can trust. It's nice to see you being ambitious about using the tools but Gaussian isn't a block box for open shell stuff. You'll maybe need to start diving into the theoretical stuff as described in Szabo and Ostlund (Modern Quantum Chemistry). They do a great description of spin contamination on pages 104 to 107.
I'm afraid you've not asked a trivial question here so good luck with it. Let me know how you get on.
--- End quote ---
Hi, I am doing organic electronics research. I am trying to compare the substituent effect using some model compounds in DFT. We observed a difference in stability for organic radical cation in terms of electrical conductivity. For example, compound A has basic thiophene unit and its conductivity would decay over a time scale of several days while we assum the radical cationic of compound A may somehow be destabilized by its electronic structure especially at the C-H bond on thiophene . For compound B, it gives out a stable conductivity for months, we assume that the methoxy groups can somhow stabilize the structure.
From the electron spin density diagram, we can see the spin is located on the C-H bond of the thiophene in compound A. I wonder if I can use this as an evidence to suggest the following radical cation dissociation at the C-H bond to give:
1) a hydrogen radical and a parent cation ( H• + P+) ; or
2) a hydrogen cation (proton) and a parent radical ( H+ + P•)
If the above mechanism really happen, a conductive compound can no longer have a delocalized polaron (or radical cation) along the pi-conjugated backbone, the electrical conductivity would then decrease.
The other image shows the spin density on compound B which is totally different from compound A that the methoxy group on the right hand side somehow act as a protecting group to prevent radical cation dissociation to happen.
but this is just my hypothesis right now.
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