Note: Softwares MATLAB and EasySpin are necessary for simulation of EPR spectra.

Contents

1. Install EasySpin

Download the EasySpin zip file and unpack it to a folder of your choice, e.g., C:\ or /var/myfiles/. Once unpacked, EasySpin is contained in a subfolder which in turn contains several subfolders.
Launch MATLAB and go to Home -> Set Path. Remove any folders containing older EasySpin installations from the MATLAB search path. Add the EasySpin subfolder easyspin-x.y.z/easyspin to the MATLAB search path by clicking on “Add Folder…”, selecting the easyspin-x.y.z/easyspin subfolder from your new EasySpin directory, and clicking on “Save”.
In MATLAB, type easyspin at the command prompt. This will display information about the installed version of EasySpin

2. Simulation of EPR spectrum

2.1 S = 0.5 Case

After EPR calculation with ORCA, a .prop file would be generated along with .out file. Use EasySpin’s orca2easyspin to read calculated data from .prop file.

Sys = orca2easyspin('tempo.prop')
Sys.lwpp = 1;                              % Line broadening
Exp.mwFreq = 9.4;                          % Spectrometer frequency, in GHz
Exp.Range = [325 350];                     % Lower and upper limit of the field sweep range, in mT
pepper(Sys,Exp)                            % Plot spectrum

2.2 S > 0.5 Case

Exacute following command (before % symbol) in MATLAB, after running of pepper(Sys,Exp), EPR spectrum would be displayed in current window.

Sys.S = 1;                                 % S = 1 for triplet and S = 2 for quintet states
Sys.g = 2.0023;                            % g factor
convert = 100*clight/1e6;                  % cm^-1 -> MHz conversion factor
Sys.D = [0.0100000 0.002000]*convert;      % Input D and E value, in cm^-1
Sys.lwpp = 6;                              % Gaussian-type line broadening
Exp.mwFreq = 9.4;                          % Spectrometer frequency, in GHz
Exp.Range = [100 500];                     % Lower and upper limit of the field sweep range, in mT
pepper(Sys,Exp)                            % Plot spectrum

2.3 Save numeric data from MATLAB figure

If you want to save numeric data from MATLAB figure, first, please save the EPR spectrum as MATLAB figure file (xxx.fig) and then, run following command.

open("C:\Desktop\xxx.fig");                % input the path to MATLAB figure file
lh = findall(gca,'type','line');
xc = get(lh,'xdata');
yc = get(lh,'ydata');

The x axis and y axis data would be saved in xc and yc sheet, respectively.

epr

Now, you can copy the data to Excel etc., and plot the EPR spectrum.

3. Running Matlab and EasySpin on KYUSHU-ITO Computer

3.1 Run Matlab

Make sure the XQuartz has been installed on your computer (Mac), run following command to login:

ssh -Y -i keydir/ito_id_rsa -l p10101b ito.cc.kyushu-u.ac.jp

where p10101b is your account ID. If you could see following error message in XQuartz terminal window, run ssh-keygen -R ito.cc.kyushu-u.ac.jp and then, try to login again.

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@    WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED!     @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

Execute followinf commands to run Matlab:

ulimit -v 31457280
module load matlab/R2019b
matlab

Wait several minutes, the Matlab window would be popped-up.

3.2 Install EasySpin to Matlab Path (For first time running)

Download the EasySpin installer from homepage and unzip it, and put the unzipped folder in your ITO folder, for example, the folder is located at/home/usr1/p10101b, execute command addpath /home/usr1/p10101b/easyspin-5.2.28/easyspin.

Then, execute easyspin command, if you could see follwoing information, the EasySpin has been installed.

Release:          5.2.28 (2020-01-31)
Expiry date:      31-Jan-2022
Folder:           /home/usr1/p10101b/easyspin-5.2.28/easyspin
MATLAB version:   9.7.0.1261785 (R2019b) Update 3
Platform:         Linux 3.10.0-514.26.2.el7.x86_64
mex-files:        mexa64, ok
System date:      12-Oct-2020 22:07:17
Temp dir:         /tmp/

MEMO: Simulation of EPR Spectrum with EasySpin