EPR Simulations with EasySpin - Revision history

Ballen: /* Fitting the Spectrum with EasySpin's esfit Function */

2020-03-26T05:31:15Z

Fitting the Spectrum with EasySpin's esfit Function

Ballen: /* Fitting the Spectrum with EasySpin's esfit Function */

2020-03-26T05:27:34Z

Fitting the Spectrum with EasySpin's esfit Function

Ballen: /* Fitting the Spectrum with EasySpin's esfit Function */

2020-03-26T05:26:59Z

Fitting the Spectrum with EasySpin's esfit Function

Ballen: /* Simulating the Spectrum */

2020-03-26T05:02:42Z

Simulating the Spectrum

Ballen: /* Simulating the Spectrum */

2020-03-26T04:54:51Z

Simulating the Spectrum

Ballen: /* Example 2: TEMPO */

2020-03-26T04:51:02Z

Example 2: TEMPO

Ballen: /* Example 2: TEMPO */

2020-03-26T04:27:23Z

Example 2: TEMPO

Ballen: /* Example 2: TEMPO */

2020-03-26T04:27:11Z

Example 2: TEMPO

Ballen: /* Example 2: TEMPO */

2020-03-26T04:22:01Z

Example 2: TEMPO

Ballen: /* Example 2: TEMPO */

2020-03-26T04:17:47Z

Example 2: TEMPO

@@ Line 413: / Line 413: @@
        ''esfit('regime function', spec1, M, Vary, Exp);''
-The first line allows us to specify a certain parameter that we are interested in varying (such as the Hyperfine Coupling '''A'''), as well as the range we would like to restrict the variation algorithm to. The second line calls the fitting function ''esfit''. This function takes the parameters of the regime function (in this case we will use ''garlic()''), our experimental spectrum ('''spec1'''), the simulation system ('''M'''), our varied parameters ('''Vary'''), and our Experimental Parameters ('''Exp'''). (More on esfit above...)
+The first line allows us to specify a certain parameter that we are interested in varying (such as the Hyperfine Coupling '''A'''), as well as the range we would like to restrict the variation algorithm to. The second line calls the fitting function ''esfit''. This function takes the parameters of the regime function (in this case we will use ''garlic()''), our experimental spectrum ('''spec1'''), the simulation system ('''M'''), our varied parameters ('''Vary'''), and our Experimental Parameters ('''Exp'''). [[EPR_Simulations_with_EasySpin#Fitting_EPR_Spectra_with_EasySpin|(More on esfit above...)]]
 Replace these lines with the following lines:

@@ Line 417: / Line 417: @@
 Replace these lines with the following lines:
-Vary.A = [5, 5];
+     ''Vary.A = [5, 5];''
-Vary.lwpp = [0.01 0.01];
+     ''Vary.lwpp = [0.01 0.01];''
-esfit('garlic', spec1, M, Vary, Exp);
+     ''esfit('garlic', spec1, M, Vary, Exp);''
 Now execute the code and you should see the following window:

← Older revision		Revision as of 05:26, 26 March 2020
Line 407:		Line 407:

	==== Fitting the Spectrum with EasySpin's ''esfit'' Function ====		==== Fitting the Spectrum with EasySpin's ''esfit'' Function ====
		+
		+	Now that you've obtained an approximate simulation in EasySpin, we can exploit its robust fitting functionality. At the bottom of the template file, you should see the following lines:
		+
		+	''Vary.parameter = [Variation Range];''
		+	''esfit('regime function', spec1, M, Vary, Exp);''
		+
		+	The first line allows us to specify a certain parameter that we are interested in varying (such as the Hyperfine Coupling '''A'''), as well as the range we would like to restrict the variation algorithm to. The second line calls the fitting function ''esfit''. This function takes the parameters of the regime function (in this case we will use ''garlic()''), our experimental spectrum ('''spec1'''), the simulation system ('''M'''), our varied parameters ('''Vary'''), and our Experimental Parameters ('''Exp'''). (More on esfit above...)
		+
		+	Replace these lines with the following lines:
		+
		+	Vary.A = [5, 5];
		+	Vary.lwpp = [0.01 0.01];
		+	esfit('garlic', spec1, M, Vary, Exp);
		+
		+	Now execute the code and you should see the following window:
		+
		+	[[File:LSQ_screen.png\|1200px]]
		+
		+	Feel free to play around with these different parameters. They are explained in detail above. When you're ready to run the fitting procedure, select the "Start" button and watch the fitting algorithm work its magic! If you obtained a successful fit, you will see a green spectrum like this:
		+
		+	[[File:Successful_LSQ.png\|1200px]]
		+
		+	If you'd like to save your parameters, you can do so selecting "Save Parameter Set", allowing you to set these parameters as the starting point for additional fittings as necessary. You can also export these parameters to your workspace, allowing you to update your original simulation code.
		+
		+	Congratulations on completing the EPR Tutorial! By no means is this tutorial exhaustive, it intends to serve as an introduction to the world of EPR simulation. You're now prepared to go into the lab, collect a spectrum, and simulate some data!

@@ Line 372: / Line 372: @@
 ==== Simulating the Spectrum ====
-[[File:TEMPOStructure.png|right|200px|Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]
+[[File:TEMPOStructure.png|horizontal:right|vertical:center|thumb|200px|Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]
 TEMPO is a nitroxide that is commonly encountered in the field of EPR. Its spectrum serves as an excellent example of an isotropic signal displaying hyperfine coupling. This adds another layer of difficulty to the procedure used in the DPPH spectrum above. The hyperfine coupling arises from delocalization of the radical across both the oxygen and nitrogen atoms. The experimental spectrum is displayed below. Nitrogen-14 has nuclear spin of I = 1, which accounts for the three lines in the spectrum. Note that there are also some satellite peaks located on each side of each of the three peaks.
@@ Line 392: / Line 390: @@
 * TEMPO is an organic radical, so you can safely guess that the principle g-value will be around 2.0. If you'd rather handle this directly, you can utilize the following relationship between the magnetic field, microwave radiation, and g-value to calculate a g-value to use for your guess:
-[[File:Gvalconversion.png|200px]]
+[[File:Gvalconversion.png|vertical:center|200px]]
 * As previously mentioned, TEMPO exhibits hyperfine coupling. This means that you will have to define a nucleus in the M.A line. Recall from above that EasySpin thinks about Hyperfine Couplings in units of MHz. If you prefer to think about these values in terms of Magnetic Field units (Gauss or milliTesla), you can use the mt2mhz() to wrap your input as follows:
@@ Line 400: / Line 398: @@
 Note that you can estimate the hyperfine splitting directly from the spectrum and then convert to MHz with the following equation:
-[[File:HFCC_conversion.png|400px]]
+[[File:HFCC_conversion.png|250px]]
 * Play with the Hyperfine Coupling Constant ('''A'''), line width ('''lwpp'''), '''g''', and the scaling factor until you have a sufficient fit of the main triplet signal. Once you've successfully simulate the triplet, you may move onto the satellite peaks. (Hint: what splits a single signal into two signals?)

@@ Line 372: / Line 372: @@
 ==== Simulating the Spectrum ====
-[[File:TEMPOStructure.png|200px|Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]
+[[File:TEMPOStructure.png|right|200px|Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]
 '''Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)'''

← Older revision		Revision as of 04:27, 26 March 2020
Line 371:		Line 371:

	[[File:TEMPOStructure.png\|200px\|Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]		[[File:TEMPOStructure.png\|200px\|Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]
		+
	Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)		Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)

@@ Line 370: / Line 370: @@
 === Example 2: TEMPO ===
-[[File:TEMPOStructure.png|frame|20px|Caption:Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]
+[[File:TEMPOStructure.png|200px|Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)]]
-[[File:TEMPOspec.png|frame|110px|Caption:EPR Spectrum of TEMPO]]
+Structure of 2,2,6,6-Tetramethylpiperidinyloxyl (TEMPO)
-TEMPO is a nitroxide that is commonly encountered in the field of EPR. Its spectrum serves as an excellent example of an isotropic signal displaying hyperfine coupling. This adds another layer of difficulty to the procedure used in the DPPH spectrum above. The hyperfine coupling arises from delocalization of the radical across both the oxygen and nitrogen atoms. Nitrogen-14 has nuclear spin of I = 1, which accounts for the three lines in the spectrum. Note that there are also some satellite peaks located on each side of each of the three peaks.
+TEMPO is a nitroxide that is commonly encountered in the field of EPR. Its spectrum serves as an excellent example of an isotropic signal displaying hyperfine coupling. This adds another layer of difficulty to the procedure used in the DPPH spectrum above. The hyperfine coupling arises from delocalization of the radical across both the oxygen and nitrogen atoms. The experimental spectrum is displayed below. Nitrogen-14 has nuclear spin of I = 1, which accounts for the three lines in the spectrum. Note that there are also some satellite peaks located on each side of each of the three peaks.
 Now, let's get started with the simulation:
@@ Line 395: / Line 397: @@
 Note that you can estimate the hyperfine splitting directly from the spectrum and then convert to MHz with the following equation:
-[[File:HFCC_conversion.png|200px]]
+[[File:HFCC_conversion.png|400px]]
 * Play with the Hyperfine Coupling Constant ('''A'''), line width ('''lwpp'''), '''g''', and the scaling factor until you have a sufficient fit of the main triplet signal. Once you've successfully simulate the triplet, you may move onto the satellite peaks.