SpinWorks is a program that will process 1 and 2 dimensional data
on personal computers. In addition it can perform spectral simulations to
determine chemical shifts and J-couplings on second-order spectra as well as
analyze dynamic events. To download SpinWorks
go to http://www.umanitoba.ca/chemistry/nmr/spinworks/ Toward
the bottom left hand part of the page click on You can download
SpinWorks here. Click on the file SpinWorks_300.zip. Once the program downloads, a new
window may appear that shows Open With
CompressedFolder (default) Click the OK
button. A new window will appear. Click on the SW3_install icon. Follow the Setup Wizard. When the window Select Installation Folder comes up
choose a different folder than Program
Files to store your SpinWorks_3 program.
Make sure it has no spaces, such as C:\NMR\SpinWorks_3\
Once the SpinWorks_3 icon
appears on your desktop click on it. At the top of the display click on Options then Set Start-up Options… Set the values of External Module Path and Writable
Scratch Path to C:\NMR\SpinWorks_3. Make
sure the Auto Save and Auto Load buttons are checked. Click OK to exit. You may uninstall SpinWorks_3 by going to the download
icon You can download
SpinWorks here. clicking on SpinWorks_300.zip
and the SW3_install icon. Then click on Remove Spin_Works3, then Finish.
It’s important to note that simulations will fail if the path of any
folder to the experimental data contains a blank space, so don’t save data in a
folder such as “My Documents”, rather a folder such as “c:\NMR” will work. When simulating without
experimental data, the path to the scratch file (set in the Options-> Set
Start Up Options… dialog) should also have no blanks. Make sure that whatever
folder you use is not read only. These rules apply only to simulations. For
normal 1 and 2D processing blanks may be left in paths. What follows is a
brief introduction to the SpinWorks program. For further details please see the
1D Data Processing
- Reading in data. Click on the SpinWorks 3 icon that has been installed on your desktop. Press the File directory at the top of the
display. Then Open an fid (eg C:\NMR\SpinWorks_3\BrukerData\odcb\2\fid which has been
provided with the SpinWorks_3 program).
The other parameter files must be present for SpinWorks to recognize the data,
so you must download the entire directory and not just the file fid to your computer. The fid (or
spectrum) will appear on the screen.
- Processing data. To look at the
processing parameters click on the green Edit Pars icon to the right middle part of the Spinworks_3 screen. You can set
line broadening, window functions, size, and other parameters in this
window. When you’re done click the OK
button in the lower right hand corner. Then hit the green Process and a fourier transform
with the designated processing will be carried out. Once the data has been
processed it will be read in as a transformed spectrum each time so don’t
worry if you don’t see your fid.
You can zoom in on your data by left clicking to the left of the spectral
region and then left clicking to the right of the spectral region. The
green vertical line will turn red each time. Then click on the blue Zoom icon in the top right portion
of the screen. To return to the full spectrum press the blue Full icon.
- Phasing. You can automatically
phase your spectrum by clicking on the green AutoPhase icon. To manually phase the spectrum, first Zoom in on your spectrum. You may
increase the intensity of the peaks by pressing the yellow + button in the
upper right hand of the display (Expt).
Press the yellow Phase button.
A pivot point will appear below the spectrum. Adjust the course and fine
zero order phase around the pivot point, then adjust the course and fine
first order phase correction for the rest of the spectrum. Click the Apply + Exit icon.
- Automatic Baseline Correction. First
left click on the yellow BL Point icon
and define at least six points in the spectrum by left clicking on regions
which have no peaks. A white line will appear beneath each point. Next
click on the red Return button.
To enter the automatic baseline correction mode click on Processing at the top of the
display, then click on Fully
Automatic Baseline Correction.
- Integration. To integrate a
spectrum, press the yellow Integrate
button in the bottom right hand corner. An Integration Dialog box will appear. Left click to the left of
a line you want to integrate, then left click to the right of that line.
Continue the same procedure for all the peaks you want to integrate. To
calibrate a particular peak, move the vertical green line till it
intersects an intensity value displayed at the bottom of the peak. Left
click the mouse. Adjust the calibration intensity by typing a new value to
the right of the Calibrate button
in the Integration Dialog box..
Left click on an individual integral value then under Delete
click on the Current button
to delete an individual integral. Click on All to delete all integrals. You may also get a printable List of integrals.
- PPM calibration. To calibrate the
ppm scale, Zoom in on the
desired peak, move the green vertical line over the peak and left click.
The green vertical line will turn red. Press the Peak Pick menu at the top, then the Calibrate… menu. In the Calibrate
Spectrum display enter the ppm value of your calibration peak, then
- Peak Picking. To set the minimum
level for peak picking , click on the green PP Minimum button on the display. A pink horizontal line will
appear. Adjust the height for
minimum peak picking by left clicking at the desired level on the screen. Click
on the Peak Pick menu at the
top of the display then on Pick Peaks and Append to List. The chosen
peaks will appear on screen and also in a List which may be displayed and saved from the Peak Pick menu. You may move from
higher to lower thresholds by clicking Pick Peaks and Append to List and add new peaks to your list.
Click the pink Return button to
the right to return to the PP
Minimum mode.. Zooming in
on various regions may make things easier by setting the threshold for
each region. New picked peaks will be appended to your list. Peaks in
local regions or the entire set may be deleted using the Peak Pick menu and Clear Peaks in Region or Clear Peak List.
- Title. A title may be added by
clicking the Edit menu at the
top of the display and then the Plot
- Printing. To print, press File, then Print… Plotting parameters are listed under Edit, then Plot Options and Parameters… You may see how your
spectrum will look after making any changes by clicking File then Print Preview.
- Saving spectra. Press Edit then Copy Metafile to file… and put in a filename. The file will be
saved in the .EMF format.
2D Data Processing
- Reading in data. Click File, then Open at the top of the display. The data set, “2D H-1/X correlation
via double inept transfer”, is provided with the SpinWorks_3 program: …SpinWorks_3\BrukerData\ strychnine\3\ser. Make sure the
entire file and not only the ser file
is read in. Processing parameters may be changed from the green Edit Pars button. To process the
data click on the green Proc. Both button.
To zoom in on a particular region, move the green crosshair to the upper
left hand section of transformed 2D data and left click. A red crosshair
will appear. Left click on the lower right hand portion of the spectrum to
enclose the data in a red box. Press the blue Zoom button. To adjust the intensity of the peaks press the
yellow + and – buttons in the upper right hand corner. The blue Range + and – buttons will adjust
the number of levels displayed.
- PPM calibration. To calibrate the
ppm values in the F1 and F2 directions, left click on a peak of known ppm
values. A red cross will appear. Press the yellow Calibrate button to the lower right of the display and fill in
- Phasing. To phase a spectrum first
pick out a group of rows. Left
click the blue button to the right that says Col
until Row appears and click on
it. Click on Row. Now go through the spectrum
right clicking on several rows to get a good sampling of data. Next left
click on the yellow Phase button.
First phase using the course and fine zero
order phase correction. Then use the course and fine first order phase correction. When
you’re done hit the Apply and exit button.
Answer Yes when the new box
appears. Click the blue Clear
button to erase the spectra displayed
on the screen and hit the blue Col button. Proceed as above to phase
the spectra in the F1 dimension.
- Linear Prediction. Linear prediction is used to improve the
resolution and Signal to Noise in the F1 dimension of 2D spectra (not in
the F2 dimension). It works well when the F1 dimension has been shortened
to save time during acquisition and will not improve data that has rung
out to the noise level. The preset parameters should work fine for most
data sets. First display a number of columns (F1 data) as outlined in the Phasing section above. Hit the Edit Pars button before processing
and the Edit Processing Parameters window
will appear. Click the F1
(Evolution) tab at the top. In the Linear Prediction area click on Forward
Complex in the drop down window.
Set Input to half the
number of time domain points and Pred:
to twice that number. (This should be done automatically). A Coef: value of 8 or 16 is fine. To
speed up calculation, lower the value of the Cutoff. Press the OK button
at the bottom of the Edit
Processing Parameters window. Then press the green Proc. Both button. You can see the
peaks have become narrower in the F1 dimension.
- Integration. To integrate peaks
left click on the yellow Integrate
button to the right of the display. An Integration Dialog will appear. Left click at the upper left
hand corner of a peak. The crosshair will turn red. Left click at the lower
right hand corner of a peak so the peak has been “boxed in”. Press Integrate under 2D Integration and Label. Proceed
to integrate the other peaks. Labels may be added as well by first
defining a Label, then
integrating. A List of
integrals is also available. Integral calibration does not seem available
at this time
- Peak Picking. To Peak Pick
click on the blue Row, Column, Label
button till Label appears
then click on Label. Right
click on a peak, the window
Peak Assignment will appear. Type in a
designation (a number or name) for the peak then click OK. The peaks will be saved to a
list which may be viewed and saved under List in the Peak Pick menu
at the top of the display. There doesn’t appear to be automatic 2-D peak
picking at this time.
- Projections. To view the F1 and F2
projections click the pull down menus at the top of the display next to F2(and F1) Trace Off and set these
to F2(and F1) Trace Proj.
- Print. Print the data by clicking
on the File menu at the top of
the page, then Print… (or Print
Preview). Plot Options and
Parameters… may be changed by clicking on the Edit menu.
Determining chemical shifts and J-couplings from your
Analysis of AA’BB’
system ortho dichlorobenzene:
will fail if the path of any folder to the experimental data contains a blank
space. Make sure that whatever folder you use is not read only. When simulating
without experimental data, the path to the scratch file (set in the
Options-> Set Start Up Options… dialog) should also have no blanks.
the SpinWorks_3 application. An odcb
sample fid has been provided. Click File,
Open and follow the path to: …/BrukerData/odcb/2/fid. Click on the green Edit Pars icon and make sure that No Window function is being used. Click
OK to leave the Edit Processing Parameters window. Click Process to fourier transform (FT)
the fid. Zoom in on both groups of
in the spin system odcb_ni at:
C:/NMR/SpinWorks_3/BrukerData/odcb/2/odcb_ni, by clicking File, then Read Spin System File...
You can view the parameters by clicking Spin System at the top of the display, then Edit chemical shifts... To view the chemical shift values in ppm,
click on the ppm button under Shift Unit. The 7.54 ppm value is the
“center of mass” for downfield pair of peaks (A,A’), and the 7.32 value is the
upfield pair (B,B’).Two fold symmetry is designated by the 2*1 notation in the table. The C2 symmetry axis runs
between the two chlorines. In this symmetric spin system AA’BB’, J(A’B’) will
automatically be set equal to J(AB) and J(A’B) will be taken to be equal to
J(AB’). Click OK to exit and then under Spin
System click on the Edit J(Scalar)
Couplings line and observe these. J(1,1) = J(AA’) = 0.3 Hz, J(1,2) = J(A,B)
= 9 Hz, J(2,1) = (A,B’) = 3 Hz, and J(2,2) = J(A’,B’) = 9 Hz. Click OK to save and exit.
Spin System click on Edit Simulation Options and DNMR parameters….
Under Simulation Display set Display linewidth (Hz) to 0.05 Hz then
hit OK button.
the Options menu at the top of the
display, then Set Start Up Options… Make sure the External Module Path and the Writable
Scratch Path are set to the proper path where the simulated data is found (with
no spaces in path names eg C:\NMR\SpinWorks_3.
Click the Simulation line then Run NUMMRIT Simulation. A simulated
spectrum will appear above your experimental data. You can move the spectra up
and down by moving the mouse cursor to the spectrum till a double arrow
appears. Then press the left mouse and reposition the spectrum. The size of
each spectrum can be readjusted with the two sets of + and
– buttons in the upper right hand
corner of the display. Note: If a previous simulation was run and red
assignment lines are present click on the Simulation menu then Delete Assigned
Peaks in Region.
5. Assign matching peaks between the two spectra. The simulated
and experimental spectra may not be lined up properly. Align the two spectra by
moving the green vertical line to the center of the left and right groups of
experimental peaks and noting the frequency in the upper left display (~7.4 ppm
and 7.2 ppm). Click on the Spin System menu
and then Edit chemical shifts... Press
the ppm button under Shift unit at
the bottom left hand corner of the display
and change the lower value to 7.2 and the higher value to 7.4 ppm. Click OK and run the simulation again. The
simulated spectrum should shift to line up approximately with the experimental
spectrum.. Zoom in on the right group of peaks. Move the red frequency line to
the peak furthest on the right of the simulated spectrum with the right and
left keyboard arrows. If the cursor is off screen a red box will appear at the
left or right bottom of the display indicating which direction the arrows
should be pressed. Then move the green line with the mouse to the matching line
on the experimental spectrum and right click. A red line will connect the two
peaks. With the left keyboard arrow move the red frequency line to the next
peak on the left. Right click the next experimental peak it lines up with. The
peaks may not line up identically on the ppm scale. Don’t worry about this as
the simulation will take care of any offsets. If you left click and the
vertical red lines appear, just continue left clicking till they’re gone and
continue. Run through all the peaks of the first chemical shift region. If you
make a mistake with an assignment just move the green line to the desired location
and reclick the right mouse button. In this first region the third pair of
simulated peaks is a doublet while the third set of peaks of the experimental
data is a singlet. Assign both peaks of the simulated set to the single
experimental peak When completed click the blue Full button and Zoom in
on the left chemical shift region and do the same procedure. To delete assignments
click the Simulation menu then Delete Assigned
Peaks in Region.
Click on the Spin
System menu and in the Edit Chemical
Shifts and Edit Scalar (J)couplings lines
check the Iterate boxes for each
assigned value. Then click the OK button. In the Spin System menu click Edit
Simulation Options and DNMR Parameters… Make sure the Optimize, Autoassign, and Autoignore
boxes are checked. Click OK.
click Run NUMMRIT Simulation. If
the simulation worked the spectra should be lined up. Load the new parameters
by clicking Simulation then Load Optimized Parameters and rerun the
simulation by clicking Simulation then
Run NUMMRIT Simulation Look at the
simulation output (Simulation, List
Simulation Output). Check the RMS deviation between the simulated and
experimental spectra at the bottom of the page:
for isotopic species 1
2155.296 2155.310 -0.014 1.71312
2158.765 2158.787 -0.022 1.67910
2158.879 2158.842 0.037 1.65734
2161.064 2161.070 -0.006 1.80108
The calculated chemical shifts and coupling constants are
listed towards the end of the Simulation,
List Simulation Ouput file.
parameters after 4 iterations are:
v = v[Ho] 2160.859 Hz. +/- 0.0052 Hz.
v = v[Hm] 2224.083 Hz. +/- 0.0055 Hz.
j = j[Ho][Ho] 0.314 Hz. +/- 0.0075 Hz.
j = j[Ho][Hm] 8.071 Hz. +/- 0.0164 Hz.
j = j[Hm][Ho] 1.521 Hz. +/- 0.0038 Hz.
j = j[Hm][Hm] 7.498 Hz. +/- 0.0091 Hz.
Save the new spin system to disk (File: Save Spin System As) and save the assigned transitions (File: Save Assigned Transitions As).