Guide to Operation of

Bruker EleXsys E500 EPR spectrometer

By Lingchao Zhu and Robert Shanks
Last updated: July 31, 2019 (HH)

I. Intro
This is a simple and brief guide to operation of our Bruker EleXsys E500 EPR spectrometer. It
includes information on powering up the system, inserting and tuning the sample in the cavity, logging into
your account and connecting to the spectrometer, setting up experiments, changing and optimizing
parameters, finishing up on the spectrometer, as well as powering down the system. For more extensive
information on operation and optimization of parameters, please see the Elexsys E 500 User’s Manual:
Basic Operations and Elexsys E 500 User’s Manual: Advanced Operations. Copies are available in the
EPR room, 2230 Chemistry.

EPR CIC staff: Heike Hofstetter Room2201B

Robert Shanks Room2130

Check out our website for more information: epr.chem.wisc.edu

II. Powering up the system

1. Push the “Electr On” button on the magnet power supply. The green LED in the switch will light
and the five Error indicator LEDs (on right side) will all light red. Wait approximately 5 seconds
until all red Error LEDs have extinguished. (Should any red Error LED remain lit, stop and find
CIC personnel) See Figure 1.

Electr On Button Power On Button

Five Error Indicator LEDS

Figure 1. Magnet Power Supply

2. Press and hold the “Power On” switch until you hear the electrical contactor engage. You should
also note that the heat exchanger pump should be running. (This powers on the electromagnet and
pumping of cooling water for the magnet and the microwave bridge.) See Figure 1.
3. Press the green power button on the Elexsys console. The green LED on the microwave bridge will
light after approximately 10 seconds and begin to blink. After approximately 20 seconds the green
LED on the bridge lights continually. Do not attempt to connect to the spectrometer while the LED
on the microwave bridge is blinking. See Figure 2.

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 Microwave Bridge Light

Figure 2. Elexsys console ON(green)/OFF(red) button and microwave bridge

4. Log on to the acquisition PC (mambo) using your standard login & password.
5. Open the Xepr program by single clicking on the Xepr icon (make sure you don’t open two
versions of the program – check on the toolbar at the bottom).
6. Go to top Menu Bar, Acquisition -> Connect to Spectrometer, then enter “localhost” and click OK
to connect to the spectrometer console. Once connected, the “Monitoring panel” at the bottom of
the Xepr software will display, allowing you to view different functions of the spectrometer. See
Figure 3.

The magnet power supply should always be turned on before the Elexsys
console is powered on and inversely the Elexsys console should be turned off
before the magnet power supply is powered down.

Acquisition

Monitoring
Panel

Figure 3. Xepr software display

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III. Inserting and tuning the sample
Here it is assumed that the appropriate cavity is installed in the magnet and the software is
pointing to the calibration file that corresponds to this cavity. For details on proper
installation of a cavity, see 7-13 through 7-25 of the Basic Operation Manual, or consult CIC
EPR staff.

It is ESSENTIAL that the cavity does not become contaminated with paramagnetic junk!
Do NOT leave the cavity open to the outside world and make sure that anything you put
into it is clean. Clean the outer surface of your tube with a Kimwipe and the appropriate solvent prior
to inserting into the cavity. There are solid collet plugs that should be installed whenever there is no
sample in the cavity. Remember: accidents do happen; if you break a sample tube in the cavity, PLEASE
report it directly to CIC staff so that the necessary cleaning and recalibration can be done before others'
experiments are corrupted.

1. Unscrew the top blue collet cap of the cavity, and place an appropriately sized collet for your
sample in place of the solid collet that’s already there. See Figure 4.
2. Replace the screw and don’t tighten all the way until after you’ve inserted the sample. See Figure 5.
Be careful when you insert the sample tube. The space of magnet is limited and sample tube is
easy to break!

Blue collet cap

White solid collet

Figure 4. No sample status for EPR cavity

3. Sample depth can be roughly judged by holding the sample in the approximate position prior to
inserting it into the cavity. You can also adjust the sample depth by pushing or pulling the bottom
white collet support - you will need to loosen the blue collet cap at the bottom. Make sure your
sample is in the middle area of cavity (black part). See Figure 5. Adjust accordingly.

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 Most effective
area for sample
location (in black)

Bottom white
Figure 5. Sample inserted in EPR cavity collet support

4. Open the tuning panel by clicking on the tuning icon on Monitor panel(see Figure 3)
and you will immediately notice that the microwaves are in “stand by” mode(indicator
shows green)
5. Click on the “tune” button and in a few seconds, the tuning display will show on the left
6. Choose “Auto Tuning” by clicking on “up” or “down” and the spectrometer will automatically tune
your sample. When autotuning is done, the “stop” button will become green and the “operate” button
will also become green. See Figure 6.
7. To tell that your sample is fully tuned, the diode current should be at the center (at 200 mA) and the
lock should also be at the center (at 0%), both will be displayed in the Monitoring Panel. “Operate”,
“Levelled” and “Calibrated” bars should be all green; (See Figure 6) if not, repeat the autotuning and
if that also doesn’t work, you will need to manually tune (see pages 7-1 to 7-11 of the Basic
Operations Manual).
8. You may want to “touch up” the tuning, by doing “fine tuning” after autotuning. You do not need
to be in “tune” mode to fine tune. It is best to stay in “operate” mode. You should also re-tune the
sample when you change the parameters, such as microwave power.

Three green bars

Auto Tuning
Figure 6. Tuning panel and fully-tuned monitor panel

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IV. Acquiring a spectrum
1. Create a “new experiment” by clicking on in furthest left part of monitoring panel then enter
name. You can also enter the sample info at “Acquisition -> Set Sample Info”. See Figure 3.

2. Click on “Parameters to Hardware” icon to get into the interactive parameters setting
mode (in this mode parameters will be immediately activated on the spectrometer).

3. Open Acquisition Parameters by clicking on the parameters icon and parameter panel will
show up. See Figure 7.
4. Check “signal channel” parameters: make sure that the calibrated button is green. Check “field”
parameters: here you define the center of the magnetic field (in Gauss), the sweep width and the
number of points acquired (typically 1024, unless want higher resolution).
5. Check “microwave” parameters: start with an attenuation of 25dB, which corresponds to 0.62 mW.
6. Check “scan” parameters: use 1 scan to start with, can do more scans with signal averaging once
you’ve optimized signal acquisition.

7. Acquire the spectrum by clicking on the run icon

8. Center the spectrum: Acquisition -> Tools -> Center tools (or use the icon); then drag the tool to

where you want the center of the magnetic field to be; then click to run new spectrum with

new center field. To remove the tool, click on the “Remove Tool” icon
9. To zoom in on a section of your spectrum, L click and drag over this section (click on “FS” icon
at top to get back to the full screen view. See Figure 8.
10. To measure peak-to-peak Gauss, put cursor on spectrum line (cursor will become a +) and
Left&Right mouse click simultaneously & drag to a different part of the spectrum line.
11. To change to another sample after your previous experiment, click the “standby” button in the
tuning panel first to make sure the attenuation>60dB, then safely change the sample and re-tune
the instrument. See Figure 6.

Figure 7. Parameter Panel

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V. Saving & Exporting the data
1. Go to top Menu Bar: File -> Save and enter the new filename for the data set. The program will also
associate “Title” with the same dataset and typically the “title” will be identical to the experiment
name
2. Your data will be stored in /home/user(your login)/XeprFiles/Data and two files get created:
filename.DSC (parameter file – can view as text) and filename.DTA (actual data – open in
Xepr only).
3. For ASCII: Go to File -> Export ASCII, then enter a filename that is NOT identical to the
original file name (as used for saving in part V). This file may then be directly read into Excel
or any other program that handles ASCII files.
4. For ESP: Go to File -> Export ESP, then enter a new filename. This will create two files: *.par
(the parameter file) and *.spc (the spectrum). You may open this data in WinEPR, however you
need to first multiply the data by a large number (1e6) before exporting as ESP.

VI. Creating Experiments from Data Sets and Saving & Loading Experiments
You can’t just load a data set and automatically start running another spectrum because the
parameters don’t automatically transfer to the console. You need to create or load an “experiment”. You
can create a new experiment by following Part IV 1-6. You can also create experiments from previous data
sets.
1. Load the desired data set: File -> Load (and select from appropriate folder and list). You can load
multiple data sets and Xepr will give you different handle number.

2. Click on the “create experiment from data set” icon , then enter the handle number (this is the
handle number that the data set was loaded into). The handle number is the number listed before the
data name. See Figure 8.

3. Click on the “Experiment Table” icon , then click on “Save” and enter a new filename to
store the current experiment. A new file with a *.exd extension will be created and put in
/home/user(you)/XeprFiles/Acquisition folder. You can change title by type new name in “Save
as” column.
4. To load a previously saved experiment, go to the “Experiment table” and click on “Load”.
Then select your stored experiment from the list of titles or filenames.

This example shows the

handle number is 1.

Figure 8. Full screen button and handle number

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VII. Get Parameters from Data Set or Experiment
You will need to have an experiment created or loaded before carrying out the following steps. The new
parameters will show immediately in the Parameter Panel. See Figure 7.

1. Click to get parameters from data set, which has been loaded and given handle number.
Choose the handle number related to the data set you want to get in the new window. Remember,
you can have multiple data sets loaded and they will all be given different handle numbers. See
Figure 8.

2. Click to get parameter from experiment you have loaded before. Choose the experiment you

want in the drop-down list of new window. You can always check “Experiment Tool” , which
will show all the experiments you loaded.

VIII. Powering down the system

1. When you are done with the acquisition, make sure the microwave bridge is in “stand by” mode
in the Tune Panel to remove your sample! Please insert a blank collet on the top of the cavity, in
place of the sample. See Figure 4 and 6.
2. Go to Acquire -> Disconnect from spectrometer and click “OK”; if you’ve properly disconnected,
the panel at the bottom of the software interface will disappear. See Figure 3.
3. Exit the Xepr software program (File -> Exit)
4. Log out of your account on “mambo” by either right-clicking on the background -> logout OR

clicking on the (bottom left corner) -> Leave -> Logoff (top choice)
5. Turn off the console: press the red button with the “o” (now green and red buttons are same depth)
6. Turn off the magnet on the magnet power supply: press the red “off” button (you will hear the
cooling water stop circulating) See Figure 1.
7. Then press the “Electr On” with the green LED on the magnet power supply to turn it off. All the
LEDs will go dark.

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Reference: Suggested parameter sets for unknown samples
(Taken out of Elexsys E 500 User’s Manual: Basic Operations, Chapter 8, Table 8-1)

Parameter Organic Radicals Metal Ions

Microwave Power (mW) 10 10

Center Field (G) 3480 3100
Sweep Width (G) 300 6000
Receiver Gain (dB) 70 70
Modulation Frequency (kHz) 100 100
Modulation Amplitude (G) 4 4
Time Constant (ms) 327.68 327.68
Conversion Time (ms) 327.68 81.92
Resolution in X (points) 1024 4096

Caution!
It is important to know how each parameter affects the resulting spectrum. Following is a brief description
of the most important parameters. See the Elexsys E 500 User‟s Manual for more details on these.

Quick Guide of EPR Parameters

Parameter Value Note

Modulation Generally 100Khz If it is sharp line(<35mG), use
Frequency lower value to avoid distortion
Modulation ~ 1/4 of the narrowest EPR signal line Lower MA→higher resolution but
Amplitude width lower sensitivity
Modulation 0
Phase
Harmonic 1 1 → 1st derivative
Receiver Start with 60dB
Gain
Conversion Start with 5.12 ms Amount of time spends
Time integrating one data point
Time Start with 1/4 of Conversion Time If it is low S/N, use the value of
Constant Conversion Time
Sweep Time Conversion Time × Number of points
OffSet 0
Center Field Center of EPR spectrum
Sweep Width whole width of EPR spectrum
Number of Start with 1024 At least 10 data points with the
points narrowest EPR signal line
Microwave Start with the lower value(e.g. 0.6mW) Lower attenuation→higher
Power Signal intensity is proportional to √P power→may heat the sample
when saturation doesn't occur
Number of S/N is proportional to square root of
Scans Number of Scans

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Microwave Power: Be careful! High power may generate heat in your sample. An excessive
power setting, P, can cause a decrease in, or elimination of, the EPR signal due to sample saturation.
This can especially be a problem for samples with relatively long relaxation times (those with sharp
resonance lines). Signal intensity is proportional to √P in the region where saturation does not occur. It
can be a good idea to perform an experiment in which the integrated intensity is measured as a
function of power microwave power; the linear region of a plot of I vs. √P indicates suitable power
levels.

Modulation Frequency: Sharp lines can be broadened by excessive values for modulation frequency (MF).
This is usually not a problem except for very sharp lines (<35 mG), and 100 kHz MF is generally used. For a
sample with very sharp lines, use a lower MF to avoid line shape distortion. If your sample has a very long
relaxation time (T1), use MF-1>>T1.

Modulation Amplitude: Increasing the modulation amplitude (MA) will, in general, increase the EPR
signal to a point. Excessive values, those greater than the line width will broaden and distort the
resonance line. A good “rule of thumb” is to use a modulation amplitude that is approximately ¼ of the
width of the narrowest EPR line you are trying to resolve. Keep in mind that there is always a
compromise that must be made between resolving narrow lines and increasing your signal to noise ratio.
If you have a very weak signal, you may need to sacrifice resolution (e.g. by using a higher MA) in order
to even detect the signal. However, if you have a high signal to noise ratio, you may choose to use a much
lower MA in order to maximize the resolution.

Receiver Gain: The best signal-to-noise ratio (S/N) is obtained with an optimal receiver gain setting. Too
low a setting will result in poor S/N, and an excessive setting will result in a spectrum that is clipped off at
the top and bottom. Starting with 60dB is a good option and you can increase it if the signal is too low.

Conversion Time: The noise, N, in an EPR spectrum is inversely proportional to the square root of the
conversion time; therefore, noise can be filtered out to some extent via longer conversion time values.
The conversion time is actually the amount of time the analog-to-digital converter spends integrating at
one field position (data point) before moving to the next one. If you need to detect lines that are very
intense as well as well lines that are very weak within the same spectrum, you will need to use a
sufficiently long conversion time. If the conversion time is too short, the smaller signals will be lost in
the steps of the digitizer.

Time Constant: The time constant (sometimes referred to as the response time) also filters out noise, N,
but here the relationship is N~1/τ, where τ is the time constant. However, if the time constant is too large,
the signal itself can be filtered out; a rule-of-thumb for undistorted line shapes is to make sure that the time
needed to scan through an EPR signal (or narrowest peak line) is >10τ. A time constant that is ¼ that of
the conversion time will guarantee that your spectrum is not distorted. For samples limited by a low signal
to noise ratio, try time constant τ≈ conversion time for better S/N.

Center Field: The center of your EPR spectrum.

Sweep Width: The whole width of your EPR spectrum.

Number of points: The number of data points will be taken in the range of sweep width. A general
rule is to make sure that you have at least 10 data points within the narrowest EPR signal line that you
are trying to resolve. This means that for EPR signals with very narrow lines you will need to increase
the number of data points that are collected for a given sweep width. However, if the lines of your EPR
signal are sufficiently wide, increasing the number of data point will not yield any additional
information, but will only result in longer sweep times.

Sweep Time: Experiment time of 1 scan = Conversion time × Number of points

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Harmonic: EPR spectra are commonly acquired as the first derivative of the absorption curve. So
usually choose 1 here. Sometimes, the hyperfine structure of the EPR signal is not resolved in
the first harmonic spectrum (1st derivative). Then you will need the second harmonic spectrum
to help resolve some of the structure of the EPR signal by changing the value to 2.

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