chili

Simulation of field- and frequency-sweep cw EPR spectra in the slow-motional regime.

Syntax
chili(Sys,Exp)
spec = chili(...)
[B,spec] = chili(...)
... = chili(Sys,Exp,Opt)

See also the user guide on how to use chili.

Description

chili computes cw EPR spectra in the slow-motional regime. The simulation is based on solving the Stochastic Liouville equation in a basis of rotational eigenfunctions. chili supports arbitrary spin systems.

chili takes up to three input arguments

If no input argument is given, a short help summary is shown (same as when typing help chili).

Up to two output arguments are returned:

If no output argument is given, chili plots the spectrum.

chili can simulate field-swept spectra as well as frequency-swept spectra. For field-swept spectra, specify Exp.mwFreq (in GHz), for frequency-swept spectra specify Exp.Field (in mT).

Input: Spin system

Sys is a structure containing the parameters of the spin system. Only S=1/2 systems are supported. The used static parameters are g, gFrame, Nucs, A, AFrame. The nuclear quadrupole interaction (specified in Q and QFrame) is neglected. See the documentation on spin system structures for details.

For simulating a multi-component mixture, Sys should be a cell array of spin systems, e.g. {Sys1,Sys2} for a two-component mixture. Each of the component spin systems should have a field weight that specifies the weight of the corresponding component in the final spectrum.

Sys should contain dynamic parameters relevant to the motional simulation. One of the field tcorr, logtcorr, Diff or logDiff should be given. If more than one of these is given, the first in the list logtcorr, tcorr, logDiff, Diff takes precedence over the other(s).

tcorr
Rotational correlation time, in seconds.

For example,

Sys.tcorr = 1e-9;         % isotropic diffusion, 1ns correlation time
Sys.tcorr = [5 1]*1e-9;   % axial anisotropic diffusion, 5ns around x and y axes, 1ns around z
Sys.tcorr = [5 4 1]*1e-9; % rhombic anisotropic diffusion

Instead of tcorr, Diff can be used, see below. If tcorr is given, Diff is ignored. The correlation time tcorr and the diffusion rate Diff are related by tcorr = 1/(6*Diff).

logtcorr
Base-10 logarithm of the correlation time, offering an alternative way to input the correlation time. If given, tcorr, logDiff and Diff are ignored.
Use this instead of tcorr for least-squares fitting with esfit.
Diff
Rotational diffusion rates (principal values of the rotational diffusion tensor), in second-1. Diff is ignored if logtcorr, tcorr or logDiff is given.
logDiff
Base-10 logarithm of Diff. If given, Diff is ignored.
Use this instead of Diff for least-squares fitting with esfit.
DiffFrame
3-element vector [a b c] containing the Euler angles, in radians, describing the orientation of the rotational diffusion tensor in the molecular frame. DiffFrame gives the angles for the transformation of the molecular frame into the rotational diffusion tensor eigenframe. See frames for more details.

In addition to the rotational dynamics, convolutional line broadening can be included using Sys.lw or Sys.lwpp.

lwpp
1- or 2-element array of peak-to-peak (PP) linewidths (all in mT).
lwpp takes precedence over lw.
lw
1- or 2-element array of FWHM linewidths (all in mT).
lwpp takes precedence over lw.

If there is an ordering potential, it should be given in Sys.lambda.

lambda
An array of coefficients for the orienting potential, with up to five elements, [lambda20 lambda22 lambda40 lambda42 lambda44], corresponding to the five linear combination coefficients λ2,0, λ2,2, λ4,0, λ4,2, and λ4,4 (the symbols c or ε are used in the literature as well) for the ordering potential U(Ω) = - kB T ΣL,KλL,K(DL0,K+DL0,-K), where the DLM,K are Wigner functions.

If you give less than five numbers, the omitted ones are assumed to be zero.

The frame of the ordering potential is assumed to be collinear with that of the rotational diffusion tensor.

For details about this type of ordering potential, see K.A. Earle & D.E. Budil, Calculating Slow-Motion ESR Spectra of Spin-Labeled Polymers, in: S. Schlick: Advanced ESR Methods in Polymer Research, Wiley, 2006.

For concentrated solutions, it is possible to include Heisenberg exchange:

Exchange
Effective Heisenberg spin exchange frequency, in MHz. Implements a simple contact-exchange model, see eq. (A27) from Meirovitch et al, J.Chem.Phys.77, 3915-3938. See also Freed, in:Spin Labeling (ed L.J. Berliner), 1976, p.68.
Input: Experimental parameters

The experiment structure Exp contains all parameters relating to the experiment. These settings are identical for all cw EPR simulation functions (pepper, chili, garlic). See the page on cw EPR experimental parameters.

Input: Simulation options

Opt, the options structure, collects all settings relating to the algorithm used and the behaviour of the function. The most important settings are:

Verbosity
0 (default), 1
Determines how much information chili prints to the screen. If Opt.Verbosity=0, is is completely silent. 1 prints details about the progress of the computation.
LLKM
4-element vector [evenLmax oddLmax Kmax Mmax]
Specifies the rotational basis size by giving the maximum values for, in that order, even L, odd L, K and M. K and M must be less than or equal to the maximum value of L.
If this field is not specified, chili automatically picks a medium-sized basis. This is adequate for many, but certainly not all, cases. In general, the basis needs to be larger for slower motions and can be smaller for faster motions. It is stronly advised to vary these settings to check whether the simulated spectrum is converged.
nKnots
Number of orientations used in a powder simulation. Default is 5. Increase this value if the orienting potential coefficients Sys.lambda are large.
LiouvMethod
This specifies which method is use to construct the Liouville matrix. The two possible values are 'Freed' and 'general'. The Freed method is very fast, but limited to one electron spin with S=1/2 and up to two nuclei. Also, the nuclear quadrupole interaction is neglected. On the other hand, the general method works for any spin system, but is not as fast. By default, chili uses the Freed method if applicable and falls back to the general method otherwise.
PostConvNucs
This specifies which nuclei should be excluded from the Stochastic Liouville equation (SLE) simulation and only included in the final spectrum perturbationally, via post-convolution of the SLE-simulated spectrum with an isotropic stick spectrum of the nuclei marked for post-convolution. E.g. If Sys.Nucs = '14N,1H,1H,1H' and Opt.PostConvNucs = [2 3 4], the only the nitrogen is used in the SLE simulation, and all the protons are included via post-convolution.

Post-convolution is useful for including the effect of nuclei with small hyperfine couplings in spin systems with many nuclei that are too large to be handled by the SLE solver. Nuclei with large hyperfine couplings should never be treated via post-convolution. Only nuclei should be treated by post-convolution for which the hyperfine couplings (and anisotropies) are small enough to put them in the fast-motion regime, close to the isotropic limit, for the given rotational correlation time in Sys.tcorr etc.

More specialized settings are:

Allocation
Array containing two numbers, [maxElements maxRows], telling chili how much memory to allocate for the Liouvillian matrix. maxElements is the maxmium number of non-zero elements, maxRows is the maximum number of rows (the dimension of Liouville space). Default is [5e6 2e5]. Increase these values if chili complains.
Example

The cw EPR spectrum of a slow tumbling nitroxide radical can be simulated with the following lines.

Sys = struct('g',[2.008 2.0061 2.0027],'Nucs','14N','A',[16 16 86]);
Sys.tcorr = 1e-9;  % 1 ns
Exp = struct('mwFreq',9.5);
chili(Sys,Exp);
Algorithm

chili solves the Stochastic Liouville equation (SLE) in the eigenframe of the diffusion tensor and in an eigenbasis of the diffusion operator. The eigenfunctions are normalized Wigner rotation functions DLK,M(Ω) with -L≤K,M≤L. The number of basis functions is determined by maximum values of even L, odd L, K and M. The larger these values, the larger the basis and the more accurate the spectrum.

chili computes EPR line positions to first order, which is appropriate for most organic radicals. It is inaccurate for transition metal complexes, e.g. Cu2+ or VO2+. For the diffusion, both secular and nonsecular terms are included.

If the spin system has S=1/2 and contains no more than two nuclei, chili be default uses a fast method to construct the Liouvillian matrix that is based on the software from the Freed lab at Cornell (Opt.Method='Freed'). For all other cases, the general code is used to construct the Liouvillian matrix.

Post-convolution works as follows: First, the SLE is used to simulate the spectrum of all nuclei except those marked for post-convolution. Next, the isotropic stick spectrum due to all post-convolution nuclei is simulated and convolved with the SLE-simulated spectrum to give the final spectrum.

For full details of the various algorithms see

See also

esfit, fastmotion, garlic