Instructions for Remote Access to the NMR from the Chemistry Computer Lab

1. Login to the computer with user as chem student and password popeye.

2. Run the X-Win 32 program by double clicking on the icon; if the icon is not on the desktop, then go to the start menu and select programs to find the file. Once the program is launched, you will not see a new screen because the program runs in the background.

3. Now double click the putty icon to launch the program. Click on NMR in the lower box and then click load, followed by open. A new window will come up with a login prompt. Each computer has a number on the front of the tower. Add this number to 140 and then login as chem141 (assuming you are working on computer 1), chem142, chem143, etc., and press enter. Now enter the password chem343 and hit enter. Type x followed by enter. The prompt should now read ≥input display server name:≤, type in the ip address for the computer, (ex. 131.230.99.157, this number may be found on the top of the computer tower) and hit enter. At the next prompt, type vnmrj and hit enter.

4. Go to step 5.

Using VNMR Software

5. You should now see the Vnmrj screen, if the putty screen is still in the foreground, then click on the Vnmrj screen to hide putty. You should see a list of data files in the upper left portion of the screen, if you cannot find the appropriate files, then change the directory to (/export/home/chem140/vnmrsys/data); this may be done by clicking on the blue arrow to move up one directory. Once you are in the correct directory and have found your file folder, then either double click on the folder or click on it with the left mouse button and drag the folder to the black NMR screen to the right. After releasing the mouse, the NMR spectrum should appear in the screen.

6. The spectrum that initially appears may not represent the full spectrum, so use the mouse to click on the textbox above the NMR spectrum and then type f and hit return. Now the full spectrum should be displayed, although the ppm scale may not be visible or accurate. Therefore, you need to reference the ppm scale to TMS (tetramethylsilane is at 0 ppm) or chloroform (7.24 ppm). If you do not see the ppm scale, then click the scale icon just to the left of the spectrum, now you should see the ppm scale underneath your spectrum. Then locate the reference peak, which is furthest to the right for TMS at 0 ppm. If you do not see a TMS peak, then you may try to find the chloroform peak and set that at 7.24 ppm. Usually the TMS and chloroform peaks are fairly small compared to the peaks due to your compound. In order to set the reference peak, click on the spectrum with the left mouse button to bring up a red vertical cursor. Now move that cursor over the reference peak and then type nl (nl makes the computer place the cursor exactly at the tip of the peak). Now click on the process tab (just below the spectrum) and then click display. In the right-middle portion of that box you will see a place to type in the chemical shift of your reference peak (just below Reference cursor to). First use the pull-down tab to select ppm and then type in the appropriate value for your reference peak (default is 0.00 ppm), then click on by cursor. Now the ppm scale should change so that the TMS peak is at 0 ppm.

For ¹³C spectra, you will see three peaks of equal height for chloroform, reference the middle peak at 77.0 ppm. Make sure the pull-down tab is set to ppm and hit enter after typing in 77.0.

7. Now adjust the spectrum to the region that you are interested in viewing and printing. You can set this region by clicking on the expansion button in the upper left corner, just to the left of the spectrum (icon has two red cursors). Click this icon until you get two vertical cursors on the screen. Then adjust the left cursor with the left mouse button and the right cursor with the right mouse button. After you have selected the region of the spectrum that you would like to expand and print, then click on the expansion icon (magnifying glass). At this point you may wish to increase or decrease the height of your peaks. To do this, move the arrow cursor over (or under) a peak and click the middle mouse button. This should move the entire spectrum up or down depending on the location of your cursor. You can also hold the middle button in and move the spectrum up or down with the mouse.

8. The software may automatically integrate the peaks, however, often it also integrates small peaks due to impurities. Therefore, it is better to manually integrate the appropriate peaks by clicking on the partial integral, just to the left of the spectrum. Then type cz in the textbox and hit return. This should give all the integrals in one line, some of which may be off the screen. You can adjust the height of these lines by using the middle mouse button to bring all the integrals onto the same screen. Next, click the integral resets button and then start at the left part of the spectrum by placing the cursor just to the left of the first peak and clicking the left mouse button, then move the cursor just to the right of that peak and click the left mouse button again. Integrate the remaining peaks in the same fashion. If you make a mistake, you can type cz and start the integration over. After integrating the peaks, type isadj in the textbox. If you would like to get rid of the integrals, then click on the full integral followed by the no integral icon. Note that you should NOT integrate ¹³C spectra as the integration does not accurately tell the number of carbons.

9. After you have integrated the peaks it is a good idea to also print out a list of your peaks so that you can calculate coupling constants for signals that are split by adjacent protons. To do this, first click on the upper integral icon twice to eliminate the integrals. Then click on the yellow threshold icon and you should see a horizontal line going through the spectrum. You can adjust the height of that line by clicking the left mouse button. Set the line so that it is below all of your peaks, but above the baseline. Then type dpf to see if the software has recognized all the peaks that you want (you may notice that all the icons to the left have disappeared, to bring these back, just click on the lower blue icon to the left of the textbox). If you have too many peaks, then reset the threshold line so that it is higher and then type dpf again. Conversely you can lower the line to detect more peaks. In rare circumstances the software does not detect a peak even after adjusting the yellow threshold line below the peak. In these cases you can click on the single cursor icon and then adjust the red vertical cursor so that it is over the peak. The yellow box marked cr just below your ppm scale tells you exactly where the peak is. However, the peak list is mainly for calculating coupling constants from doublets, triplets, etc., so if you have a singlet, then it is not a big deal if you donπt see it listed in your table, as you can just look at your ppm scale to get figure out its chemical shift. The table is not visible on the computer screen, but it will be printed out in the upper right corner. After you have set the threshold, then you can click on the partial integral icon to bring the integrals back on screen.

10. Now you are ready to print the spectrum. First, select a printer under the utilities tab (top of screen), then select printers. Choose vittplotter and vittprinter in the drop-down menu, then click OK (you only need to do this once for each login session). Under the black screen you should see a process tab. Under the process tab select plot and make sure that Plot Peak Frequencies as a list is checked. When you are ready to print hit the automatic plot page button. The printout can be picked up in Neckers room 222 (one floor up next to the main chem office). If this room is locked or the printer is not working, then you may try to print to the dyerlabprinter in Neckers 307.

Exit procedure

11. Under the utilities tab, click Exit Vnmrj, then close the X-win 32 window by right mouse clicking on the icon in the lower right corner of the screen. Now quit the putty program. It is very important that you logoff properly, otherwise the next student may not be able to access the data.

Summary

The normal steps in generating a spectrum are as follows: a) load spectrum, b) display the ppm scale, c)set a reference peak, e) expand the spectra to the region that you wish to view and print, f) integrate, g) set the threshold, h) plot, i) logout.

Having Problems

The most common problem students have is that they cannot access the data even though the Vnmrj software seems to be working. This is usually because the last student did not logout properly. In this case the TA will have to reset that account, so please notify the TA when a computer is not working properly. Feel free to contact Prof. Dyer or either of the two TAπs if you need help.