Max T. Rogers NMR Tip of the Week Archives
Welcome to the the Max T. Rogers Tip Archives. Each week we distribute an e-mail alert detailing the latest status of our instrumentation. The alert also includes various tips related to the facility, which are designed to facilitate the use of the Varian spectrometers. This resource page contains all the archived tips of the week, which have been sent since June 23, 2003. Scroll through the list below to find the desired tip.
Our NMR instruments aren't getting younger and unexpected data loss may occur. Additionally, from time to time we will need to free up disk space by removing some older files, which may include your data. We will warn everybody before this occurs, but it's best to be prepared. To save on a ZIP disk (also posted in room 240):
I. Login on a workstation in room 240 (the middle two) using Common Desktop Environment (CDE).
II. Insert your ZIP disk in the the ZIP drive. Wait for the ZIP window to appear (about 30 sec).
III. Open the "Home folder" window. (Left click the "files" icon in the bottom toolbar). All your datafiles will be shown on this window.
IV. Copying files:
a. To copy one file (ABC.fid for example):
Use the left mouse button to drag the "ABC.fid" file into the ZIP window. To see the ABC.fid filename on the ZIP window: Select VIEW, then UPDATE.
b. To copy multiple files:
Keep the 'Control' button pressed down while selecting and dragging files.
When you are finished select FILES, then EJECT in the ZIP window. Please logout properly. To save data on your PC desktop or laptop or your MAC:
I. Open a browser window (e.g. Microsoft Internet Explorer).
II. In the address bar, type 'ftp://username@bes' and hit ENTER.
A new window will popup titled "Login as".
III. For the new window titled "Login as", in the "username" box, ensure that it's the correct name (e.g. if you ftp://xyz1@bes, the username should be 'xyz1'), if not change it. In the "Password" box, type the correct password and click OK.
IV. The original browser window should now show your data folders for the desired instrument.
Click and drag the files/folders to the desired folder on your hard drive.
V. To access another instrument, change the username in the address bar to the desired instrument and hit ENTER. Continue using via Step III.
Your peak shape is dependent on the homogeneity of the NMR magnetic field. By shimming, you are attempting to make the field homogeneous at your sample. Many variables affect your peak shape. Those that are most important to the user are:
1. amount of solvent: too little and you will have trouble shimming, particularly with Z2. You should use at least 5 cm of solvent in the tube.
2. viscosity of solvent: the higher the viscosity, the broader your lines.
3. particulates in your sample: floating, undissolved matter in your sample will have deleterious effects on your lineshape. If necessary, filter your sample.
4. paramagnetic impurities: small particles of metals or other paramagnetic materials will cause line broadening. This can be minimized by not using metal spatulas to transfer your sample. Dissolved oxygen, which is paramagnetic, also causes some line broadening. Degas your sample if you require the narrowest lines possible.
5. the quality of the NMR tube: imperfections and unevenness in the NMR tube glass will lead to a degradation in your lineshape. It is best to use NMR tubes that are rated for the field you are using (e.g. on the VRX-500, use a tube rated for 500 MHz or better)
For a guide on shimming and the affect of each shim set on lineshape (e.g. poor Z1 causes symmetric broadening), see:
Remember to start by typing ‘fixshims’. It is best to only vary Z1 and Z2, then autoshim on Z1, Z2, and Z3. This should be good for most samples.
To Save your own Shim Settings:
I. Shim as usual. See above for a basic procedure.
then hit RETURN
To Retrieve your Saved Shim Settings:
Did you ever want to look at two spectra at the same time and determine any differences (e.g. to see if changing the probe temp affects peak location or to look at the progress of a reaction by comparing to the starting material)? It's easy with the addi program.
NOTE: Prior to using addi, you should be sure you don't have any valuable unsaved spectra, parameters in exp5 because exp5 is the workspace used for this program. If you have never used exp5, you should be fine.
To view two spectra at a time and see the difference between them:
I. In VNMR, type: jexp1 and hit Return
II. Acquire or load a saved file as usual and type: wft f and hit Return.
III. type: clradd and hit Return. This clears exp5, which is the default add/sub buffer. IV. type: spadd and hit Return. This adds the current spectrum to the add/sub buffer (i.e. exp5).
V. type: jexp2 and hit Return. Acquire or load a saved file as usual and type: wft f and hit Return.
VI. type: addi and hit Return. This will add the spectrum in exp2 to the add/sub program.
You should now see three stacked spectra:
The bottom spectrum is from the current window (in this case it's from exp2);
the middle spectrum is the one from exp1 that you added to the add\sub buffer using spadd;
the top spectrum is the sum of the two spectra (this is the default setting).
Interacting with Spectra:
On the bottom middle of the screen, you have two display terms; active: and mode:.
active: designates which spectrum is currently selected. Any actions you take, such as scaling size with the middle mouse, will change the active spectrum. To select a different spectrum, click on [Select]. Note that active: will change each time.
mode: designates the action taken to generate the result spectrum (top spectrum) from the other spectra. The initial mode is add, which is the sum of the two spectra. To switch to sub (subtraction of the spectra) or min (minimum points between each spectra), just click on [sub] (note that mode is now sub), click on [min] to get min, etc.
Printing the result (e.g. Difference between two spectra):
I. Once you have chosen the result you want, click [save].
II. type: jexp5 ds and hit Return. Now you have the result of either adding two spectra or subtracting two spectra.
III. Print, expand, etc. in the usual manner.
(e.g. type: pl pscale page)
Did you ever want to stack multiple spectra and save them as an array (e.g. the stacked view and plotting for DEPT) for printing and displaying? Well, you’re in luck because it can be done. You can stack as many spectra as you want either horizontally or vertically, view individual spectra, and then save them as an array for later use.
TO PRINT STACKED SPECTRA: You will need to create an arrayed dataset, which will allow you to view and print all stacked spectra.
Note: type what’s in the ‘’ and hit Return.
Important Commands for Arrayed Spectra:
ds(#) - where # is the spectrum number in the array. The first spectrum is 1, the second is 2, etc. (e.g. ds(1) to display first spectrum.
dssa - displays all spectra vertically
dssh - displays all spectra horizontally
dssl - displays the spectrum number(#) to be used with ds(#)
pl(‘all’) - print all stacked spectra
I. Load the spectra in exp1 and add them to an array: type ‘jexp1’ -
join experiment 1
II. Type ‘clradd’ - clear the add/sub buffer in exp5. This will erase anything in exp5.
III. Click Main Menu => File and select the first desired spectrum and click Load.
IV. Type ‘add’ - adds FID to add/sub buffer.
V. For adding all additional spectra, click File, select the desired spectrum, click Load, and type ‘add('new')’.
VI. Join exp5 and create array parameters: type ‘jexp5’ - join experiment 5.
VII. type ‘gain='y' ‘- turns off autogain, which is not allowed in arrayed experiments.
VIII. type ‘d2=1,2,3’... - sets arrayed variable. Use same number of variables as spectra. For example, if you want 10 spectra, type ‘d2=1,2,3,4,5,6,7,8,9,10’.
IX. Type ‘calcdim’ - calculates the array dimension.
X. Type ‘groupcopy('current','processed','acquisition')’ - updates parameters.
XI. Type ‘ai’ - resets to absolute intensity mode.
XII. Type ‘wft dssa’ - Fourier Transform all FIDs and display stacked spectra vertically. If you want horizontal stacks, type ‘dssh’.
XIII. Type ‘svf('your filename')’ to save the arrayed spectra.
You may need to adjust the phasing. If phasing is incorrect, type ‘ds(1)’ (this displays the first spectrum), or click Interactive. Type ‘aph’.
To adjust the scale of each spectrum: type ‘ds(spectrum number)’ (where spectrum number is an integer. For the first spectrum, spectrum number is 1: ds(1); for the second spectrum, spectrum number is 2: ds(2); etc.). Adjust the scale as usual. To check, type dssa.
XIV. To print, use standard printing commands except replace pl with pl('all'). For example, pl(‘all’) pscale pltext page.
Last week I described how to create an ‘artificial’ array in order to stack spectra. This week I will describe how to create a true arrayed experiment. An arrayed experiment allows the user to run multiple experiments in a single session with no need for changing parameters each time a value needs modification. Why would you want to run an arrayed experiment? There are many circumstances where an arrayed experiment is useful. Did you know that the DEPT macro is an arrayed experiment? Or perhaps you wish to determine a 90∞ pulse for a HMQC experiment or you would like to acquire spectra of a compound at multiple temperatures or maybe you want to take a spectrum of a reaction every 10 minutes and you don’t want to sit around for 3 hours. I will use the last example to set up an arrayed experiment for a kinetics experiment.
Internal Standard: I will need an internal standard that does not interfere with the kinetics of the reaction and that does not have peaks that overlap with my starting material or product. Furthermore, I should use an internal standard in roughly a one-to-one proton equivalent to the substrate (a proton equivalent is equal to moles/# of protons). It is also important that the internal standard be somewhat similar to the compounds being measured to ensure that the T1s are not too dissimilar.
Remember those T1s: If I do not allow for complete relaxation between pulses, I will not get accurate integration and hence incorrect data. T1s for aromatic and alkene protons can be longer than for alkyl protons. As a general rule, a delay of at least 30 seconds between scans should be enough for complete relaxation. If waiting 30 seconds between scans is not feasible, then I would use the Ernst command, which will calculate the appropriate pulse width based on a given pw90, at, d1, and T1. A good value for the T1 for Ernst would be 30 seconds; thus, I would type ernst(30).
Instructions for Kinetics Experiments Performed in NMR Probe: Type text in ‘’ and hit Return
There are two possibilities for running a simple array: using a macro or using command line execution.
USING THE ARRAY MACRO: This will allow you to array parameters with set intervals between scans.
I. Lock and shim on your sample or a blank sample with the appropriate solvent. The second option is for when the reaction you want to monitor occurs at room temperature or lower.
II. Take a quick scan (nt=1) to ensure proper shimming.
III. Type ‘ernst(30)’. Set nt=8 or to another value which will be repeated in IVc. Type ‘su time’. Note the time, you will need this.
IV. Set VT controller to desired temperature. Type ‘temp=# su’, where # is your desired temperature in ∞C. Most instruments, except for the VXR-300, which can be set to 100 ∞C, have a temperature limit of between 0 and 50 ∞C. If you need to do temperatures outside of this range, contact us at ext. 792. REMEMBER: DO NOT EXCEED THE BOILING POINT OF YOUR SOLVENT! Allow the temperature to equilibrate prior to beginning your kinetics array. You will need to shim at the temperature of your kinetics run to ensure the best results.
V. Type gain=’n’. If this doesn’t work, type ‘gain=30’. Autogain is not allowed for arrayed experiments.
VI. Setup the arrayed experiment:
a. Type ‘array’
b. Parameter to be arrayed: ‘pad’
i. This is the preacquisition delay which will set the interval between successive scans.
c. Number of increments:
i. This is the total number of spectra or data points you want. If I want to monitor a reaction every 10 minutes for 3 hours, I would need 18, so I type ‘18’.
d. Enter Starting Value:
i. This is the time between each individual data point (a data point consists of 8 scans) or spectrum. To calculate this value, take the time in seconds you want between spectra and subtract the time determined in step III. Thus, for an example, I want to take spectra at 10 minute intervals, which is every 600 seconds. Step III gave me a value of 16 seconds; therefore, my pad should be 600 – 16 or 584 seconds. I type ‘584’.
e. Enter Array increment:
i. Type ‘0’. This sets the increment to zero, which means the preacquisition delay will always stay the same. If you typed 1, the pad would increase by 1 second each successive spectrum.
VII. Run the experiment:
a. Insert your sample. Type ‘i’ and ‘go’. You won’t be allowed to lock your sample as it is already acquiring. By locking and shimming your sample or a blank prior to the arrayed experiment, you have set Z0 where it will lock. The instrument should lock after a short period. At this time you can shim to get the best possible spectrum. The first scan will occur after the pad you set. You can shim throughout the experiment if you desire. It’s a good idea to check the timing between each data acquisition using a stopwatch.
USING COMMAND LINE EXECUTION FOR AN ARRAY:
This allows you to have differing values between each data point or spectrum.
I. Follow steps I-V above.
II. Type, for example, when you want to take a spectrum every 10 minutes (see VI. d. above) ‘pad=584,584,584,584,584,584’ to take six spectra with about 10 minutes between each data point. Each number represents an experiment with the preacquisition delay (pad) in seconds set for that number. If I wanted to take 5 measurements at 10 minutes, 15 minutes, 17 minutes, 20 minutes, and 40 minutes, (assuming the actual acquisition takes 16 seconds, see VI. d.) I would type ‘pad=584,284,104,174,1184’. Remember that the pad is the time between each data point.
III. Run the experiment:
a. Insert your sample. Type ‘i’ and ‘go’. You won’t be allowed to lock your sample as it is already acquiring. By locking and shimming your sample or a blank prior to the arrayed experiment, you have set Z0 where it will lock. The instrument should lock after a short period. At this time you can shim to get the best possible spectrum. The first scan will occur after the pad you set. You can shim throughout the experiment if you desire.
Save your arrayed experiment as you would a normal experiment (i.e. svf(‘filename’)).
Important Commands for Arrayed Spectra:
ds(#) - displays spectrum #, where # is the spectrum number in the array. The first spectrum is 1, the second is 2, etc. (e.g. ds(1) to display first spectrum).
dssa - displays all spectra vertically
dssh - displays all spectra horizontally
dssl - displays the spectrum number(#) to be used with ds(#)
pl(‘all’) - print all stacked spectra
The odd colors for your VNMR interface are usually a result of having too many windows/applications open. Since VNMR is generally the last to be opened, it is given the last dregs of color available, which turn out to be pretty awful. You should close all unnecessary applications prior to running VNMR.
TO FIX THE DISPLAY COLORS OF VNMR:
I. After logging-in to the session and prior to running VNMR, close all windows that pop up (e.g. Netscape, Solaris Registration, Terminals, etc.).
a. If you have the Solaris Registration window open every time you log-in, you can disable it by clicking More Information=>Never Register=>Never Register.
II. Click on the VNMR icon. The colors should be fine. If not or if you want your own colors, do the following:
a. Type ‘color’ and hit Return. A color palette will appear.
b. Click on the button for the item you wish to change the color (e.g. background, spectrum, etc.) and then click on the desired color.
c. When completed, enter a filename for the name color scheme and click save. If you want this new scheme to be the default, save the file as DEFAULT.
If Console is unresponsive to Commands, follow the procedure below:
1. With the right mouse button, click once on the Solaris desktop background to reveal a menu. Click on Programs or Tools, then over to select Terminal… A Terminal window will pop-up.
2. In the Terminal window, type ‘su acqproc’ and hit Return. You will get a message indicating that acqproc is being ‘killed’. Also, in the ACQUISITION STATUS window in VNMR, STATUS should now read “inactive”.
3. Proceed to the NMR console, which is the big grayish box. See below for location of reset button for various instruments.
4. Push the reset button. See location information at end of document to find reset button.
5. After pressing the reset button, wait for at least 60 seconds.
6. In the terminal window type ‘su acqproc’ and hit Return. This will take a few moments. Look at the ACQUISITION STATUS window in VNMR. Wait for STATUS to read “idle”.
7. In the VNMR command line (i.e. where you usually type e), type ‘su’ and hit Return. The NMR should now be ready for use. Repeat if this does not restore system.
8. For VXR-500: If the proceeding procedure did not work, repeat the above procedure, but instead of pushing the reset button, flip the switch directly below the ‘reset button’ to off. Wait about 20 seconds and switch it to ‘on’. Follow Steps 4-6.
LOCATION OF RESET BUTTON FOR EACH INSTRUMENT:
Anubis: VXR-500 (subbasement)
Reset button is in the big grayish box to the right of the computer. Open the middle door and look for a button on the left with a hand written label “reset button”.
Ra: Inova-300 (subbasement)
Reset button is in the grey box to the left of the computer, open the left door and look for the hand written blue arrows to the middle left. The red button below 'reset' at the far left where the blue arrows point is the button.
Hathor: G-300 (5th floor)
Open the door of the box to the right of the computer. Look for the switch with the hand-written word, 'reset'.
Maat: VXR-300 (2nd floor)
Reset button is on the front right side of the box to the right of the computer. Look for an arrow pointing toward a black button.
Khufu: Inova-300 (2nd floor)
Open the left door of the box on the wall with windows. Look at the middle left and just above the blue plug. The small white button above the letters RST is the button.
Have you ever set your threshold below a set of peaks, typed ‘dpf’, and only got a few of the peaks to be picked? It’s happened to me on a couple of times. Well, that doesn’t have to happen. The default noise level filter (noise_mult) is 3, which will give only a certain fraction of the peaks. Try ‘dpf(1)’ or even ‘dpf(0)’. These will give you more peaks. If you want less, try ‘dpf(5)’. How about the pesky negative peaks that you don’t want? Don’t pick them by typing ‘dpf(‘pos’)’ to pick positive peaks only. Below is a list of what you can do with dpf.
EXAMPLES OF DPF USAGE: First set the yellow threshold line below the desired peaks.
Important: Remember to refresh the VNMR screen before entering a new dpf command or you will see two sets of peak labels. Typing ‘ds’ or clicking Interactive will refresh the screen.
Type ‘dpf(#)’, where # is a number below 3 to increase number of peaks picked.
Type ‘dpf(#)’, where # is a number above 3 to decrease number of peaks picked.
Type ‘dpf(‘pos’)’ to pick positive peaks only. You can include the # argument to change number of positive peaks picked: e.g. type ‘dpf(‘pos’,1)’.
Type ‘dpf(‘top’)’ to place the peak labels at the top of the page.
Type ‘dpf(‘leader’, #), where # is a number in mm for the labels to be placed above the peak. Default is 20 mm. Type, for example, ‘dpf(‘leader’,30)’ to move the peak labels up.
Combine several to make your ideal peak label:
For example: dpf(‘pos’,0,’top’) will give all positive peaks below threshold with labels at the top of the spectrum.
dpf(‘pos’,5,’leader’,10) will give selected positive peaks above the threshold with the peak labels on 10mm leaders.
Have you ever been in a rush and didn’t have the time to mark off your integral regions? Well, there is a Varian cure: the ‘region’ command breaks up a spectrum into integral regions. I’ve tried it and it’s not so bad, especially for quick spectra. Give it a try.
To automatically break the integrals into specific regions:
I. Click Part Integral.
II. Type ‘region’. This will break the integral into peak regions.
III. If you need tighter integrals to get more peaks, type ‘region(10,1)’. The numbers in the parenthesis describe the tail length and relative number of integrals. The default values are sw/10 and 12, respectively.
Other settings for the ‘region’ command are:
Full syntax: region(‘tail_length, relative_number, threshold, number_points, tail_size)
tail_length: length in Hz that is added to the beginning and end of each integral region. The default value is sw/10.
relative_number: number that, in combination with other factors, governs the relative number of regions to be found. The default value is 12. A value of 1 would give more regions; a value of 100 would give fewer regions.
threshold: a sensitivity factor used to decide if a data point is large enough, relative to the noise level, to qualify as part of a peak. The default value is 0.6.
number_points: governs the number of successive data points, normally from 7 to 40 points, that must qualify as part of a peak.
tail_size: a number that governs whether two spectral areas that contain peaks are close enough to be regarded as a single region.
Examples: region – uses default values.
region(10,1) – sets the tail length to 10 Hz and the relative number to 1. This gives more peaks.
region(-1,0,0,2) – sets tail_length, relative_number, and threshold to their default values. Sets number_points to 2. This would be used for spectra with large spectral widths.
IV. After the region command is used, reference your integrals as usual.
Currently, most of us add text to the spectrum by typing, “text(‘name of spectrum\\solvent instrument\\date etc.’)”, where the \\ signify a new line. There is an easier way to enter and modify text. You just need to type: gettext. This will execute a simple text editor. You will be able to see and edit text that is already there. Furthermore, you will be able to add text using the Return key to start a new line. Try it, you’ll like it!
TO USE THE WINDOW BASED TEXT INPUT: Type: gettext and hit Return. It may take a few seconds for the grey window to pop-up.
You may get the following error message,’The OpenWindows environment may no longer support…’. This is not a problem, simply check the box next to the line,’Check here to disable this message,” and click OK; it will not appear again.
1. Add text to the large text box and hit Return when you want to start a new line. When completed, Click OK and your text are ready for plotting.
2. If you need to edit your text, type, gettext, and edit as you would in Word. Click OK when completed.
3. Plotting is done as always; the pltext command. To plot it in the top right corner, use pltext(150,150) in your plot statement (e.g. pl pscale pll pltext(150,150) page).
Tuning the VXR-500. General Considerations:
1. Be sure that you setup the correct experiment (e.g. Setup=>C13,CDCl3 for carbon) and type ‘su’ after setup.
2. Be sure to carefully follow the instructions on the probe.
3. Do NOT force the tuning rods. They are FRAGILE. If you feel resistance when turning the rod, you probably have reached the end and should turn the rod in the opposite direction.
4. Always start tuning by turning the shorter rod (Red for Proton. Gold for Carbon).
5. In general, you need only turn the shorter of the two rods for either Proton or Carbon.
6. If you need to turn both rods, start by turning the shorter one until you get a minimum on the meter. Then,…
a. Turn the longer one (Blue for proton. Black for Carbon) in a direction opposite to what you turned the short rod. Turn the long one to the minimum and continue turning in the same direction until the meter reading goes up a bit (5 with the lower knob set to 60).
b. Now turn the short rod to minimize the meter reading and continue turning in the same direction until the meter reading goes up a bit.
c. Return to the long rod and turn to minimize. Turn past the minimum as before.
d. Repeat for both the short and long rod until the meter reading is minimized.
e. If this process does not lead to a minimum, try reversing the directions you were turning the rods.
The temperature that is displayed in the Acquisition window
is generally not completely accurate. This can be caused by many factors,
including fluctuations in VT gas flow and inaccuracy in the thermocouple.
If you require exact temperature measurement for kinetics or for other reasons,
you can use the chemical shift temperature dependence of either ethylene
glycol or methanol to accurately calculate the actual probe temperature.
The facility has the appropriate samples to perform a temperature calibration.
For experiments with multiple temperatures, you should create a calibration
curve. The calibration curve can be used for more than a single run.
Procedure for Temperature Calibration:
I. Insert your sample. Lock and shim as usual.
II. Eject your sample and insert the calibration standard. Make sure that the calibration standard is centered properly (i.e. the solvent should be centered about the two white lines in the gauge).
a. The sealed samples are located in B-8. Use the ethylene glycol sample for high-temperature calibration or methanol for low-temperature calibration.
b. Note: these samples do not contain deuterated solvent. Do not attempt to lock or shim. The shimming you did for your sample will be sufficient.
III. Enter your desired temperature. For example, I might type ‘temp=40 su’ to set the temp to 40 degrees Celsius.
IV. Allow sufficient time for the probe and sample temperature to equilibrate (at least 10 minutes).
V. Acquire a 1H spectrum (nt=1). Place the two cursors on top of the peaks.
VI. Type ‘tempcal(‘e’)’ for ethylene glycol or ‘tempcal(‘m’)’ for methanol.
VII. After hitting Return, the calculated temperature will be displayed above the VNMR command line.
VIII. Repeat for all desired temperatures.
Use autoshim to fix those funny peak shapes (can require several
I. Insert, lock, and shim in the usual manner.
II. Click on auto to the right of SHIM:.
III. Choose L>M and Z1,Z2,Z3.
IV. Click Start. The button will change to Stop. The autoshimming will take several minutes. Autoshimming will be complete when the button is Start again.
V. Close the Acquisition window and acquire a spectrum.
VI. If you are satisfied with the shimming, save them by typing svs(‘filename’).
VII. To retrieve them for later use, type rts(‘filename’) su.
To Print an Expanded Region (inset) with your Spectrum:
I. Process your spectrum as usual and type pl pscale pir pltext. DO NOT type page. The page command sends the job to the printer. You want to hold this job until you add your inset(s).
II. Put the cursors around the region for which you wish to print an expansion.
III. Type inset. The expanded view will appear on the screen. This view is now interactive and can be manipulated like usual. The full spectrum is no longer interactive.
a. Use the left mouse button to set the horizontal position.
b. Use the middle mouse button to set height.
c. Use the right mouse button to set size.
d. Use the vp command to set vertical position (e.g. type vp=40 to set the inset at 40 mm)
e. If you expand the inset and wish to reposition the new expansion, click sc wc and move as described before.
IV. To print the inset: type pl pscale pir etc. If you would like another inset, repeat the process described above ensuring that you type pl pscale pir after each inset.
V. When completed, type page.
VI. To reset the spectrum to the full page, type vp=12 f full.
February 17, 2009