SpinWorks

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 SpinWorks_3 documentation.


1D Data Processing

  1. 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.
  1. 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.
  1. 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.
  1. 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.
  1. 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.
  1. 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 click OK.
  1. 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.
  1. Title. A title may be added by clicking the Edit menu at the top of the display and then the Plot Title display.
  1. 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.
  1. 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

  1. 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.
  1. 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 the values.
  1. 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.
  1. 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.
  1. 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
  1. 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.
  1. 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.
  1. 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.

Spinworks Spectrum Simulation

Determining chemical shifts and J-couplings from your spectra.

Analysis of   AA’BB’ system ortho dichlorobenzene:                                       

Remember: Simulations 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.

1.      Open 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 peaks.

2.      Read 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.

3.      Under 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.

4.      Click 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.

 

6.      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.

7.      Under Simulation 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:

Transitions for isotopic species 1

                                           RMS deviation

  18   2155.296   2155.310    -0.014    1.71312

    6   2158.765   2158.787    -0.022    1.67910

  26   2158.879   2158.842     0.037    1.65734

  12   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.

 

***  Final parameters after 4 iterations are:

   v[1] =         v[Ho]                             2160.859 Hz. +/-        0.0052 Hz.

   v[2] =         v[Hm]                            2224.083 Hz. +/-        0.0055 Hz.

   j[1][1] =     j[Ho][Ho]                          0.314 Hz. +/-           0.0075 Hz.

   j[1][2] =     j[Ho][Hm]                         8.071 Hz. +/-           0.0164 Hz.

   j[2][1] =     j[Hm][Ho]                         1.521 Hz. +/-           0.0038 Hz.

   j[2][2] =     j[Hm][Hm]                        7.498 Hz. +/-           0.0091 Hz.

 

8.      Save the new spin system to disk (File: Save Spin System As) and save the assigned transitions (File: Save Assigned Transitions As).