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Chili for non-nitroxide systems
Posted: Thu Jul 21, 2016 10:54 pm
by wlinde
At the moment, I am simply playing with chili in order to simulate slow motion dynamics of iron-catechol complexes. I have a fairly naive question, centered on the following code:
Code: Select all
Sys = struct('g',[2.24 2.24 1.92],'Nucs','56Fe','A',[20,20,85]);
Sys.tcorr = 5e-10;
Exp = struct('mwFreq',4.65,'Range',[20,620],'nPoints',5e3);
chili(Sys,Exp);
Ignoring, for a moment, the fact that the numbers are not correct (I am interested in fitting them later), my question is: what am I simulating, exactly? Is it neutral Fe, Fe 2+ or Fe 3+? Is it in a high or low spin state?
Thanks for your clarification
Re: Chili for non-nitroxide systems
Posted: Fri Jul 22, 2016 6:55 am
by Matt Krzyaniak
In this case you'd be simulating an S=1/2 iron system. The specific oxidation state of the iron is somewhat irrelevant to the simulation, only the number of unpaired/interacting electrons.
Re: Chili for non-nitroxide systems
Posted: Mon Jul 25, 2016 1:10 pm
by wlinde
Great! Thank you.
How do I control the number of paired/unpaired electrons for the purpose of the simulation. I had trouble finding information about this in the documentation. Suppose, for example, that I was interested in simulation of S=5/2 iron. How could I do this?
Re: Chili for non-nitroxide systems
Posted: Tue Jul 26, 2016 1:20 pm
by joscha_nehrkorn
I am not completely sure, but I guess it is one of the first lines of the documentation about the spin system. (Spin 1/2 is a default value)
Re: Chili for non-nitroxide systems
Posted: Tue Jul 26, 2016 1:45 pm
by wlinde
Thank you. I tried that, but there appears to be no difference associated with a change in spin. I am running the following code:
Code: Select all
close all
figure(1)
Sys = struct('g',[2.24 2.24 1.92],'Nucs','56Fe','A',[20,20,85]);
Sys.tcorr = 5e-9;
Sys.S=5/2;
Exp = struct('mwFreq',4.65,'Range',[20,620],'nPoints',5e3);
chili(Sys,Exp);
figure(2)
Sys2 = struct('g',[2.24 2.24 1.92],'Nucs','56Fe','A',[20,20,85]);
Sys2.tcorr = 5e-9;
Exp2 = struct('mwFreq',4.65,'Range',[20,620],'nPoints',5e3);
chili(Sys2,Exp2);
It is clear that the spectra are identical for any timescale, but the chili literature makes it seem like high spin counts should still be supported. For instance, it says
With this setting, EasySpin will include the relevant polarization factors resulting from a thermal equilibrium population of the energy levels. For S=1/2 systems, it is not necessary to include the temperature. However, it is important in high-spin systems with large zero-field splittings, and in coupled spin systems with exchange couplings.
Does anyone have any ideas? I'm genuinely unsure what is going wrong.
Re: Chili for non-nitroxide systems
Posted: Tue Jul 26, 2016 1:45 pm
by wlinde
Thank you. I tried that, but there appears to be no difference associated with a change in spin. I am running the following code:
Code: Select all
close all
figure(1)
Sys = struct('g',[2.24 2.24 1.92],'Nucs','56Fe','A',[20,20,85]);
Sys.tcorr = 5e-9;
Sys.S=5/2;
Exp = struct('mwFreq',4.65,'Range',[20,620],'nPoints',5e3);
chili(Sys,Exp);
figure(2)
Sys2 = struct('g',[2.24 2.24 1.92],'Nucs','56Fe','A',[20,20,85]);
Sys2.tcorr = 5e-9;
Exp2 = struct('mwFreq',4.65,'Range',[20,620],'nPoints',5e3);
chili(Sys2,Exp2);
It is clear that the spectra are identical for any timescale, but the chili literature makes it seem like high spin counts should still be supported. For instance, it says
With this setting, EasySpin will include the relevant polarization factors resulting from a thermal equilibrium population of the energy levels. For S=1/2 systems, it is not necessary to include the temperature. However, it is important in high-spin systems with large zero-field splittings, and in coupled spin systems with exchange couplings.
Does anyone have any ideas? I'm genuinely unsure what is going wrong.
Re: Chili for non-nitroxide systems
Posted: Tue Jul 26, 2016 2:34 pm
by joscha_nehrkorn
Don't panic! Nothing is wrong. Check solid state spectra without hyperfine interaction for the two cases. They will and they should be identical. Look at the quote from the documentation you posted: It is about zero-field splitting. This is absent in your code, therefore there is no difference. You can add it as
This will change your spectrum strongly.
Re: Chili for non-nitroxide systems
Posted: Wed Jul 27, 2016 7:13 am
by wlinde
Ah, great. Thank you very much!