Modelling A Rigid Diradical

[ERClark]

Hello,

I'm currently trying to model CW X-Band solution EPR of a rigid diradical (a bis-nitroxide) and am struggling to set up my initial parameters and indeed work out where to start. Reading the forum, people have attempted this using both Chili (viewtopic.php?f=3&t=279) and Pepper (viewtopic.php?f=3&t=370 , viewtopic.php?f=3&t=342).

Since I want to model an isotropic system, I've used chili as a start, using the parameters below:

Code: Select all

Sys.S = [1/2, 1/2];
Sys.g = [2.0048; 2.0048];
Sys.Nucs = ['14N,14N'];
Sys.A = [45 0;0 45];  
Sys.lwpp = 0.1;
Sys.logtcorr=-9;

However, if I specify a value using Sys.J=10 (for example),I receive the error message "Reference to non-existent field 'eeFrame'." whilst using Sys.ee=10 chili runs but no meaningufl output is seen, just a flat spectrum.

If I specify anisotropic A values (Sys.A=[20 20 80 0 0 0; 0 0 0 20 20 80] , taken from Chris Wedge's post, also using Sys.ee=10) then a perfectly reasonable looking spectrum is simulated. On the other hand, if I try to use isotropic coupling defined that way (Sys.A=[40 40 40 0 0 0; 0 0 0 40 40 40]), once more I get a blank spectrum.

I am, in short, confused and sure I've misunderstood some definitions. I believe that the system described above is for a two electron system, each electron interacting only with one nucleus, and the two electrons then coupling with each other. On the other hand, I'm not sure why things break if isotropic coupling is used, nor why Sys.J does nothing but Sys.ee works even though I only specify one value and not a coupling matrix as explained in the documentation.

I suspect that I'm in over my head but I'd like to learn to swim.

[Stefan Stoll]

Please post the scripts that produce these errors, so we can have a look.

[Stefan Stoll]

The following runs without errors with the latest ES release:

Code: Select all

clear, clc

Sys.S = [1/2, 1/2];
Sys.g = [2.0048; 2.0048];
Sys.Nucs = '14N,14N';
Sys.A = [45 0;0 45]; 
Sys.lwpp = 0.1;

Sys.J = 10;

Exp.mwFreq = 9.5;
Exp.Range = [334 343];

pepper(Sys,Exp);

[ERClark]

Thanks for the reply. Here're the scripts used and their responses.

Code: Select all

Sys.S = [1/2, 1/2];
Sys.g = [2.0048; 2.0048];
Sys.Nucs = ['14N,14N'];
Sys.A = [45 0;0 45];  
Sys.lwpp = 0.1;
Sys.logtcorr=-9;
Sys.ee=10

Exp.mwFreq=9.5;
Exp.CenterSweep=[336.50 9];

chili(Sys,Exp)

This returns a flat line.

Code: Select all

Sys.S = [1/2, 1/2];
Sys.g = [2.0048; 2.0048];
Sys.Nucs = ['14N,14N'];
Sys.A=[20 20 20 0 0 0; 0 0 0 20 20 20];  
Sys.lwpp = 0.1;
Sys.logtcorr=-9;
Sys.ee=10

Exp.mwFreq=9.5;
Exp.CenterSweep=[336.50 9];

chili(Sys,Exp)

This also returns a flat lane.

Code: Select all

Sys.S = [1/2, 1/2];
Sys.g = [2.0048; 2.0048];
Sys.Nucs = ['14N,14N'];
Sys.A=[40 20 20 0 0 0; 0 0 0 40 20 20]  
Sys.lwpp = 0.1;
Sys.logtcorr=-9;
Sys.ee=10

Exp.mwFreq=9.5;
Exp.CenterSweep=[336.50 9];

chili(Sys,Exp)

This produces a plausible looking spectrum. It's really centred as the values used above were taken from some older nitroxide data of mine to use as a starting point for for learning how to define the system so all I wanted was something visible.

Code: Select all

Sys.S = [1/2, 1/2];
Sys.g = [2.0048; 2.0048];
Sys.Nucs = ['14N,14N'];
Sys.A=[40 20 20 0 0 0; 0 0 0 40 20 20]  
Sys.lwpp = 0.1;
Sys.logtcorr=-9;
Sys.J=10

Exp.mwFreq=9.5;
Exp.CenterSweep=[336.50 9];

chili(Sys,Exp)

This returns the following error message, "
Reference to non-existent field 'eeFrame'.

Error in magint (line 109)

Error in chili (line 723)

Error in chili (line 109)"

Thank you for the example script snippet - I see that it uses pepper instead of chili, so I'll use that in future.

[Stefan Stoll]

chili giving a flat line for completely isotropic systems is expected behavior. We will consider adding an error message for this case in the next version.

The error you get in your last script is a bug. We will fix it, thanks for reporting! In the meantime, add the line Sys.eeFrame = [0 0 0] to your script to make it work.