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Chemical exchange- how to?

Posted: Wed May 11, 2016 12:44 am
by katarkon
It seems that EasySpin can simulate cw spectra with chemical exchange broadening (J. Phys. Chem. A, 2013, 117 (7), pp 1439–1448 DOI: 10.1021/jp3104358). Unfortunately, there are no any documentation about this feature. Is it possible to provide some examples for this topic?

Re: Chemical exchange- how to?

Posted: Tue May 17, 2016 8:31 pm
by Stefan Stoll
This code is not officially incorporated into EasySpin yet. However, you can download it from the file exchange forum and use it.

Re: Chemical exchange- how to?

Posted: Wed May 18, 2016 1:57 am
by katarkon
Thanks a lot for amazing program.
I have some questions about it.
1. Sys.xc parameter is not described enough. I propose that it defines the order of the nuclei in the second and futher sites. Is it right?
2. It is not completely clear how to define exchange rate contants. For example, for two-site exchange k12 for direct and k21 for reverse reaction. Or k12, k21, k13, k31, k23, k32 for three-site exchange? Sys.k seems to be reduced value, is it so?
3. Is it possible to define separate linewidth and intensity for each site? Defining separate linewidth causes an error:
Error using *
Inner matrix dimensions must agree.
Error in exchange (line 233)
Exp.Range = B0 + [-1 1]*mhz2mt(freqSweepRange/2,mean(Sys.g));
Or
Error using *
Inner matrix dimensions must agree.
Error in exchange (line 362)
M0 = -Gamma*eye(nSites) + X;
Or similar errors, depending from Opt.Method value

Possible source of error is line 83:
Gamma = lwpp*pi*sqrt(3);

Re: Chemical exchange- how to?

Posted: Wed May 18, 2016 10:40 am
by Stefan Stoll
Regarding Sys.xc and how to define the exchange rates, please look through the code of the function to see how they work. We don't have any additional documentation of this. At some point, we hope to be able to revisit this function and document it properly - then it will become part of EasySpin. Regarding separate linewidths, I don't think the function supports that. You might be able to modify it to accommodate this, though.

Re: Chemical exchange- how to?

Posted: Thu May 19, 2016 2:47 am
by katarkon
I have made some minor changes in the code. Now general methods (1 and 2) seems to be working with separate lw for each site and arbitrary population. May I publish the code for testing in the corresponding topic?

Re: Chemical exchange- how to?

Posted: Thu May 19, 2016 8:29 am
by Stefan Stoll
Of course!

Re: Chemical exchange- how to?

Posted: Thu May 19, 2016 11:53 pm
by katarkon
I would like to add the possibility of working with natural isotopes mixture. If it is possible, give me corresponding code from garlic function. If not I'll try to write my own.

Re: Chemical exchange- how to?

Posted: Fri Jun 10, 2016 4:12 am
by katarkon
Now I try to simulate the spectrum with two kinds of broadening caused by chemical exchange and thumbling effect in fast-motion regime simultaneously. I propose to apply convspec function to each line spectrum during accumulation. But I have a doubt is this way correct or not.
The example of such spectrum is in attachment (exchange of two phosphoruses nuclei with a~200G and a~30G).