Department of Chemistry, University of Alberta         May 2004
NMR News 2004-02
News and tips for users of the Varian NMR systems in the Department

There are no fixed publishing dates for this newsletter; its appearance solely depends on whether there is a need to present information to the users of the spectrometers or not.

Other content of this NMR News is no longer meaningful and has been removed May 2010.



NMR data processing in the Department


m400:a "new" spectrometer for undergraduate students


sucrose (90 vs. 600 MHz)


NMR data processing in the Department Updated 2010-05-07
There are more and more possibilities for processing NMR data, aside from doing this right at the spectrometers which is the least desired way as it ties up the instrument when it could be used to acquire data (an exception, of course, is data processing while more data are acquired simultaneously!). Here is an overview of the possibilities:

1) Use one of the LINUX data stations
EB-44C: ibdw plus an independent, fully functional terminal with access to ibdw
WB-13: d500
SB-3G: d601 plus an independent, fully functional terminal

All provide 8.5 x 11 laser printer capabilities.

2) Use a Mac or PC to remotely access a UNIX server - some of this is outdated. See FAQ on SSH (2014) for updates.
With the introduction of Mac OS X, there are new possibilities for Mac users. OS X is built around a UNIX kernel and this facilitates access to the NMR computers. The user typically starts a remote X-session (X being a form of windowing software) from the Mac to the LINUX server (d601 or ibdw) and does all the work from the Mac computer. If a network printer is available in the research group, the printouts can be sent to this printer. In other words, user input and printing is done in the lab/office while the actual work of processing data is done by the LINUX servers. This approach is currently used by >10 research groups in the Department. Very popular, no doubt but there is no point trying to do this without getting a few things organized beforehand.

If you would like to add a Mac computer to this form of data processing, the following needs to be done (for PCs see below):

(a) For PCS: A computer security check, carried out by the IT people, has to demonstrate that the computer requiring access is patched and up to the latest security standards. The computer has to be inside the Department (firewall) with a permanent IP number. No access will be granted to computers outside the Department.
(b) On the Mac side, the system has to be set up to do X-sessions. Two documents in PDF format can be found here: Mac setup and actual usage.
(c) On the UNIX side, computer IPs have to be identified as friendly (see (a)) and, if desired, macros to switch to a network printer have to be created. This is done only after steps (a) and (b) have been completed.

If you are interested in this form of data processing, please provide the following information to the editor (for the LINUX side) and the IT group (for the security part):

computer name & computer IP (always starts with 129.128.)
printer name & printer IP (also starts with 129.128.)

Thanks to Doug Burr in Dr. Vederas' group for providing the "Mac-side" information needed to make this work.

Special note for PCs: unfortunately, the PC/Windows world has not yet caught up to the beauty and stability of a UNIX kernel. However, it is possible to do X-sessions with PCs as well.
Instructions on how to do this can be found here.

m400: a "new" spectrometer for undergraduate students
A  Varian Mercury 400 MHz system has been ordered. Its main function will be to provide undergraduate students with an opportunity to measure their own NMR samples instead of submitting them to the NMR service. The Mercury system is Varian's lower end product line, as opposed to the research-level Inovas. However, essentially all 1D and 2D experiments that are currently used can be performed on a Mercury including gradient experiments. m400 is a used system but only a few years old and comes with full guarantee by the manufacturer. When the University is not in session, i.e. from about mid-April to the end of August, it will also be available for graduate students and postdocs. The same will likely apply to overnight and weekend time. Although not all details are known at this stage, you will be informed in a later issue of NMR News. m400 will have the same capabilities as the i400, including 31P, and thus should help to reduce the pressure on this intensely used spectrometer.

Sucrose (90 vs. 600 MHz NMR)
You may know that the late Professor Ray Lemieux was inducted into the Canadian Science and Engineering Hall of Fame for his achievements in carbohydrate research. Dr. Lemieux joined the Department of Chemistry at the University of Alberta in 1961. One of his many milestone contributions was the full synthesis of sucrose and NMR studies to prove its structure. In today's world of superconducting magnets, it is sometimes hard to imagine what NMR was like back in those times. To illustrate this the following illustration was created and added to the Hall of Fame display. 

The 90 MHz spectrum (*) is shown on top, the 600 MHz equivalent at the bottom. Both spectra were recorded in D2O. The 600 MHz spectrum shows the quality of solvent suppression and, of course, the expected dramatic increase in signal dispersion. While the past is often referred to as the "good old days", this does certainly not apply to NMR! Other than H1g, nothing is really directly accessible for analysis at 90 MHz. Even H3f and H4f are so close at 90 MHz that they partly overlap and form a higher order spin system. Please note that only some key resonances are labeled here. A 600 MHz 2D spectrum provides, not surprisingly, a complete assignment of all protons.


Interesting is the H1f proton pair. Even at 600 MHz the chemical shift of the two protons is so similar that a very tight AB system is observed.

At first sight it looks like a singlet (which would entail that, through fast rotation, the two protons cannot be distinguished on the NMR time scale). However, the two small transition lines symmetrically located on both side of  the intense center line clearly show that this is an AB (these are neither spinning side bands nor 13C satellites!).

Through spin simulation the chemical shift difference was found to be only 0.005 ppm (3 Hz) with a geminal coupling constant of -12.5 Hz between the two protons. It is not all that often seen at such a strong field that the coupling constant between two protons is 4 times larger than their chemical shift difference. Truly higher order!

More information on higher order effects can be found in NMR News 2003-01.

A short summary about Professor Lemieux's work is provided here (courtesy of Professor David R. Bundle). The same picture as shown above but with a CPK model is also available in this summary.

For the technically and historically interested readers: 60, 80 and 90 MHz spectrometers were so-called continuous wave (CW) instruments. When sweeping through the spectrum a distinct "ringing" after an intense, narrow peak was observed if the homogeneity was good. This is missing in the 90 MHz picture but not because of homogeneity problems. This 90 MHz spectrometer was actually transformed to a Fourier Transform (FT) system and hence provides similar line characteristics (no "ringing") as modern FT systems. 

(*) We are grateful to Don White in the Department of Pharmacy for providing access to their 90 MHz FT spectrometer. It is a formidable challenge nowadays to find a field below 300 MHz and hence we are really glad we could obtain the spectrum from Pharmacy.

top of page    NMR News