Difference between revisions of "WINSIM"

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Simulation of Multiple Isotropic Spin-Trap EPR Spectra

Installing WINSIM

Public Electron Paramagnetic Resonance Software Tools

Choose the older version of WINSIM.zip and extract all...

Running a WINSIM Simulation

This is the main menu bar...

WINSIM will allow you to import an EPR data file to display along with the simulated data. In this first example, we are going to do simulations only; first select the "parameters" item under the "Simulation" tab...

Parameters

The above panel is were all simulation parameters are input. Please note the following:

1) This program can simulate up to 10 radicals in one EPR spectrum. It is very rare to have more than one radical in a spectrum, but there are cases where there is a background signal as well as a signal of interest, so...2 radicals...sometimes. To start the simulation you must select "YES"...calculate this [1] species...

2) On the right side of the parameters panel is where you enter the EPR parameters:

Set: each type/set of spins has their own parameters. For example in methane, CH₄, there is only one set of protons.

Hyperfine: this is a term which indicate the "energy" of interaction between a nuclear spin and the unparied electron.

Spin: this is the nuclear spin.

Number: how many spins are in this set

Opt: when fitting experimental EPR data an optimization routine can be run, this is where you select whether you want to optimize this parameter or not.

3) These parameters allow some fine tuning of the simulation and will be introduced later.

Simulation 1

Run a simulation for the methyl radical, CH₃^. (set 1 - check, hyperfine 15 G, Spin - 0.5, Number - 3, opt - leave as checked (but not used), click "Simulate" (bottom left)...

Sim 1 follow up...for educational purposes follow these instructions:

- change the Number to 1, and simulate...you will now see only 2 lines, displayed in a "first-derivative" signal (typical in EPR due to the detection system). The separation between these two line is 15 G (Gauss).

- Change the Number to 2, and simulate...you will now see 3 lines all separate by 15 G.

- Change the Number to 3, and simulate...you will now be back to the original EPR simulation of methyl radical; 4 lines all separate by 15 G.

Simulation 2

Run a simulation for the ethyl radical, CH₃-CH₂^....are all of these protons the same? You would need to collect the EPR signal for this radical and see if the hyperfine was the same for the protons:

If they are different, then the simulation could be setup as...

- set 1 - check, hyperfine 12 G, Spin - 0.5, Number - 2, opt - leave as checked (but not used),

- set 2 - check, hyperfine 8 G, Spin - 0.5, Number - 3, opt - leave as checked (but not used),

- click "Simulate"...

If they are all the same, then the simulation would be setup as...

(Note: for ease of setup, the simulation is still using 2 sets, but they have the same parameters, same as only 1 set with 5)

- set 1 - check, hyperfine 10 G, Spin - 0.5, Number - 2, opt - leave as checked (but not used),

- set 2 - check, hyperfine 10 G, Spin - 0.5, Number - 3, opt - leave as checked (but not used),

- click "Simulate"...

EPR Interpretation

The analysis of EPR spectra has been made considerably easier using the WINSIM (or similar) simulation software. Below are a set of general rules that all EPR spectra follow:

EPR Line Intensities and Pascal's Triangle

The intensity of EPR lines following the coefficients of the polynomial expansion, (x+1)ⁿ. Each individual nucleus results in the main EPR transition being "split" into a multiline pattern referred to as "hyperfine."

- when n=1, the splitting pattern is 1:1...as in coefficients in (x+1)¹ = "1x+1" are 1 and 1.

- when n=2, the splitting pattern is 1:2:1...as in coefficients in (x+1)² = "1x²+2x+1" are 1, 2, and 1.

- when n=3--> 1:3:3:1

Ex. Benetis, et al. (2015) methyl radical (experiment and extensive simulations)

- when n=4 --> 1:4:6:4:1

Ex. Buettner, et al. (2008) see figure 2 BQ - not the first to publish this radical

- when n=5 --> 1:5:10:10:5:1

- when n=6 --> 1:6:15:20:15:6:1 (rare to have 6 equivalent protons)

- when n=7 --> 1:7:21:35:35:21:7:1

- when n=8 --> 1:8:28:56:70:56:28:8:1

EPR Literature

Ascorbate Radical

Hydroxyl Radical

THE ORIGIN OF THE HYDROXYL RADICAL OXYGEN IN THE FENTON REACTION - 17O data

Superoxide (a radical)

Semiquinone (a radical)

Other

EVIDENCE FOR FREE RADICAL FORMATION DURING THE OXIDATION OF 29-79-DICHLOROFLUORESCIN TO THE FLUORESCENT DYE 29-79- DICHLOROFLUORESCEIN BY HORSERADISH PEROXIDASE: POSSIBLE IMPLICATIONS FOR OXIDATIVE STRESS MEASUREMENTS

@@ Line 64: / Line 64: @@
 ===EPR Line Intensities and Pascal's Triangle===
-The intensity of EPR lines following the coefficients of the polynomial expansion, (x+1)<sup>n</sup>.
+The intensity of EPR lines following the coefficients of the polynomial expansion, (x+1)<sup>n</sup>. Each individual nucleus results in the main EPR transition being "split" into a multiline pattern referred to as "hyperfine."
 :- when n=1, the splitting pattern is 1:1...as in coefficients in (x+1)<sup>1</sup> = "1x+1" are 1 and 1.
 :- when n=2, the splitting pattern is 1:2:1...as in coefficients in (x+1)<sup>2</sup> = "1x<sup>2</sup>+2x+1" are 1, 2, and 1.
-:- when n=3, the splitting pattern is 1:3:3:1...as in coefficients in (x+1)<sup>3</sup> = "1x<sup>3</sup>+3x<sup>2</sup>+3x+1" are 1, 3, 3, and 1.
+:- when n=3--> 1:3:3:1
+::*Ex. [[Media:Benetis_15a.pdf|Benetis, ''et al.'' (2015) methyl radical (experiment and extensive simulations)]]
 :- when n=4 --> 1:4:6:4:1
+::*Ex. [[Media:Buettner_2008a.pdf|Buettner, ''et al.'' (2008) see figure 2 BQ - not the first to publish this radical]]
 :- when n=5 --> 1:5:10:10:5:1
 :- when n=6 --> 1:6:15:20:15:6:1 (rare to have 6 equivalent protons)
-:-when n=8 --> 1:8:28:56:70:56:28:8:1
+::*Ex. [[Media:Weissman_75a.pdf|Weissman, ''et al.'' (1975) no EPR spectrum, 1st report of benzene radical anion with 18C6]]
-::*Ex. [[Media:Stevenson_92a.pdf|cyclooctatetraenyl radical anion]])
+::*Ex. [[Media:Stevenson_88a.pdf|Stevenson, ''et al.'' (1988) no EPR spectrum only method of prep with K/18C6/THF]]
-::*Ex. [[Media:Strauss_63a.pdf|cyclooctatetraenyl radical anion with Na hyperfine]
+:- when n=7 --> 1:7:21:35:35:21:7:1
+:- when n=8 --> 1:8:28:56:70:56:28:8:1
-Example, the methyl radical above has 3 identical protons, so the line intensity is 1:3:3:1.
+::*Ex. [[Media:Stevenson_89a.pdf|Stevenson, ''et al.'' (1989) cyclooctatetraenyl radical anion/K/HMPA]]
+::*Ex. [[Media:Stevenson_92a.pdf|Stevenson, ''et al.'' (1992) cyclooctatetraenyl radical anion]]
+::*Ex. [[Media:Strauss_63a.pdf|Struss, ''et al.'' (1963) cyclooctatetraenyl radical anion with Na hyperfine]]
-Below are a set of EPR spectra (some simulated and some experimental) to be used to practice interpreting EPR data.
 ==EPR Literature==
@@ Line 90: / Line 91: @@
 ===Superoxide (a radical)===
+===Semiquinone (a radical)===
+===Other===
 [[Media:Mason_1999a.pdf|EVIDENCE FOR FREE RADICAL FORMATION DURING THE OXIDATION
 OF 29-79-DICHLOROFLUORESCIN TO THE FLUORESCENT DYE 29-79-
 DICHLOROFLUORESCEIN BY HORSERADISH PEROXIDASE:
 POSSIBLE IMPLICATIONS FOR OXIDATIVE STRESS MEASUREMENTS]]