Function of the blog

Transforming Graduate Education With mNova NMR and mnova Reaction Monitoring

Tue, 1 May 2012 07:53:39 -0500

< download the KEYNOTE version of this talk by clicking here >
< download the PDF version of this talk by clicking here >

Education is major focus of IMSERC, and we take great care with our course for first-year Organic Chemistry graduate students, Organic Spectroscopy (Chem411). In 2012, thanks to an internal grant from Northwestern’s Office for Research, we were able to purchase a site license for Mestrelab’s suite of software, including MNova NMR, MNova MS, and NMR Predict. This software enabled us to transform our course, allowing us to:
1) Teach concepts more effectively. For instance, showing how multiplets are created by using MNova multiplet analysis tools, and showing the effects of strong coupling using NMR Predict.
2) Teach skills more effectively. Instead of teaching spectrum assignment by handing out photocopied spectra or specifying a problem number in a book, we were able to hand out raw fid’s that the students would process and analyze in the manner of researchers who had just collected data. Assignment strategy using MNova’s coordinated spectra, tables, and illustrative assignment lines, enables students to focus on the assignment task rather than making judgements about which peaks line up with which in piles of paper.
3) Train students to write effective reports. By making JACS-format presentation of spectral data easy, MNova enables us to require publication-ready lab reports and homework assignments. Not only is this good for the students and laboratories in which they will be working, their reports are very easy to grade!

The talk seemed to go over quite well with the audience, and a number of people have asked for copies of the slides. Please download them using the links above if you are interested. Thanks.

DOSY TIps/Concerns

Tue, 15 Sep 2009 12:34:17 -0500

A few days ago, my counterpart at Caltech, Dr. David VanderVelde posted a query to the AMMRL email list about how to improve his DOSY spectra. The community weighed in with a number of recommendations, which he shared, and he’s given me permission to post his summary here.

It seems the main problem with DOSY experiments is that they are easily confounded by convection within the sample. One gets around this in a few ways: turning off sample temperature control if possible, using Shigemi tubes, and using convection-compensating pulse sequences. I’ll work on assessing and fixing these problems here at NU.

Here’s David’s post:

The possibly imperfect DOSY plot is the result of subjecting your possibly
imperfect diffusion data to an inverse Laplace transform, which is
inherently not as stable, say, as the Fourier transform is at displaying
signal frequencies. My main interest was in trying to make my input data
less imperfect. A data set where the spectrum phase does not hold
constant as the gradient amplitude is ramped up is not going to give a
textbook DOSY--the phase instability is taken as a sign of convection in
the tube.

The biggest problem in our experimental setup was temperature gradients
within the sample. I believe I was doing a good deal to create these
gradients by using the FTS cooling bath to chill the VT air on our system
and then reheat to achieve regulation at 25 C. The instrument is a 600
with a protein type triple resonance HCN triax gradient probe. Running
the cooling bath all the time is fairly common, I think, on protein
instruments. For low viscosity organic solvents, this proved to be highly
counterproductive for diffusion experiments, as a pretty small temperature
gradient is enough to sustain convection. This down side may be less, or
not, apparent with aqueous protein samples, as water is much more viscous
than e.g. THF or acetonitrile. But I always took it on faith that I was
doing a good thing by using precooled air in protein experiments--now I'm
not so sure. It would seem to me that any convection would lead to signal
losses in pulse sequences with many, many gradient pulses. What I can say
for sure is that the bigger the amount of precooling (we were normally
using 15 C), and the lower the airflow, the worse the temperature
gradients become. When it was especially bad, obvious problems appear
with gradient shimming--the profiles develop large gaps in them. But
phase instability in the diffusion spectra was evident when there were no
other obvious problems with other gradient-based experiments.

I received a number of suggestions about ways to reduce the temperature
gradients within the sample, the simplest of which was just to turn off
active temperature regulation. This amazingly improved the phaseability
of the 1D spectra; I have to think the data would better define the
diffusion coefficient. The processed DOSY data did not look that much
better, however, in terms of alignment of peaks from the same molecule.
Additionally using the convection compensated pulse sequence with no
active temperature regulaion cost about half the signal overall, but gave
a significantly better DOSY. It was not clear what about the convection
compensated 1D data going in to the DOSY was better--this data also phased
well, but no better, as the data taken without convection compensation
already had a completely stable spectrum phase and flat baseline.

Other suggestions for improved temperature homogeneity included using a 3
mm probe, putting a 3 mm tube into a 5 mm probe, and using a slotted
spinner turbine which allows VT air to run completely past the sample tube
and exit out the top.

One respondent said he had been told by a vendor that the linear region of
z gradient in an xyz-gradient probe is indeed shorter than a z-only
gradient probe--something on the order of only a centimeter. He got
better results by using a Shigemi tube to put sample only in the center of
the gradient coil.

Other replies focused on postacquisition processing, including very
meticulous phase and baseline corrections to the 1D data, using the
"fiddle" function to correct for any non-Lorentzian character of the
lineshape, and using absolute value instead of phase sensitive spectra.
In high S/N spectra, baseline problems are the largest source of error,
either from the baseline not being flat, or a small peak on the tail of a
large one.

David VanderVelde
Manager, High Resolution NMR Facility, Caltech
davidv@caltech.edu

NMR Tube Shopping

Fri, 4 Sep 2009 12:24:58 -0500

When shopping for NMR tubes, what do you look for? They all look basically the same, but some are as cheap as ~$1, and others cost 30x that much. Why? And does it matter to you?

Erika Crane from the Scheidt lab just asked me for recommendations, and I thought I’d take the opportunity to do some comparison shopping and give everyone, including Erika, some help on the subject. I searched the NMR tube manufactures’ websites for specs and retail prices, plugged the data into a spreadsheet, sorted the data a few ways, and eyeballed the data to make some suggestions. (Click on the word “spreadsheet” to download the document.)

RECOMMENDATIONS:

1) For ALL uses, please buy 8”-long tubes. The A500 robot requires unchipped 7” tubes, so the moment a 7” tube get chipped, it’ll need to be thrown out. It’s always better to spend a few cents more and get an 8” tube that, when chipped, can be filed, snapped and flamed so it presents a clean edge at the top.

1) For routine use, in which you’re going to use the tube a bunch of times until it’s worn out, and where your spectrum isn’t going to be published, I recommend spending between $4 and $6 per tube. Sure there are “Economy” tubes for <$2, and they have their place: as disposable items for samples whose spectra don’t have to be very good. These would be good for routine purposes at NU:
New Era: NE-ML5-8
Norell: 506-P-8
Wilmad: WG-1228-8
Kontes: 897205-0008
Optima: NGS-400
I don’t include prices because they A) are subject to change, and B) you should talk to the
relevant sales reps to get the best academic pricing, especially if you’re buying in bulk for the lab. However, these are all in the $4-6 range.

Note that NMR tubes are usually graded by the 1H frequency of the spectrometer they’re appropriate for. “Economy” and ‘High Throughput” tubes are usually rated for 60 or 100 MHz instruments. The tubes listed above are rated for 200-400 MHz systems.

1) If you’re going for a publication-quality spectrum on A500, you should use a good pyrex tube, rated for 500 MHz. These cost maybe $12 to $18 each. If you run bunches of spectra all the time, you’d probably want to set these aside for special occasions - these are the “good china”. Here are the tubes I’d look for if I were you:
New Era: NE-UP5-8
Norell: S-5-500-8
Wilmad: 528-PP-8 or 535-PP-8
Kontes: 897241-0008
Optima: NGS-600
1) If you’re running on A600 or any higher-field instrument, I’d default to a Wilmad 535-PP-8 or 541-PP-8, though the specs on the New Era NE-SP-5-8 and Norell S-5-900-8 tubes look great, too. For experiments like these, your personal time, the time on the instrument, and the cost of making your sample dominate the experiments’ expenses, so don’t waste your time on a cheapo tube. Plan on spending $18 to $35 on a normal tube, or ~$80 on a Shigemi tube (see below).

Why these tubes? Basically, I grouped them by price range, then sorted by their specifications of “concentricity” and “camber”. You can imaging that magnetic field homogeneity is going to be affected by how well centered the tube is in the probe. Since the tube is held at one end, this factor is determined by how straight the tube is. “Camber” is a measure of how far the tube deviates from being perfectly straight. You might also imagine that homogeneity is affected by the uniformity of the glass thickness. It seems that the manufacturers are good at making both the inner and outer cross-sections of the tube very circular, but that it’s more difficult to make the inner and outer circles line up exactly. The measure of wall thickness uniformity is often “concentricity”, because the the wall is thicker on one side than the other, it’s because the inner and outer circles aren’t perfectly concentric. Here are links to more authoritative discussions from the manufacturers themselves: Wilmad, New Era, Norell.

Also, I would be remiss if I didn’t mention Shigemi tubes. These marvelous inventions elegantly enable you to cut down your sample volume to~300-330 uL. In a normal NMR sample, only the middle region of the sample is actually detected, but the solution above and below this region is necessary for preserving magnetic field homogeneity by keeping the solution/air boundaries away. In a Shigemi tube, the undetected sample is replaced with glass - special glass with magnetic susceptibility matched to your solvent’s, so the field lines pass between your sample and the glass without distortion. This is not only a great way of cutting down on your sample volume, but it also improves water suppression by eliminating stray signals from regions at the edge of the sensitive region, and improves diffusion measurement by restricting your sample to the region of greatest gradient homogeneity.

Happy shopping! If you’re a new customer you may get a tube or two as a freebie. Tell them I sent you.

- Josh

DOSY - Adventures in Diffusion NMR

Thu, 27 Aug 2009 12:26:05 -0500

Click here to download the talk in Apple’s Keynote format.

Click here to download it in Microsoft’s Powerpoint format.

Announcing Mini-zine #1: “VnmrJ the easy way”

Thu, 18 Jun 2009 12:49:49 -0500

VnmrJ is an amazing piece of software. For chemists who need quick routine spectra, and even biochemists who need huge sets of complicated data, VnmrJ offers a variety of automatic features that ease data collection. Yet it still contains a command-line user interface that hasn’t changed substantially since the mid-1990’s. Some people continue to use it this way because that’s how they were trained, and it works OK for them. But they’re missing out!

This user guide describes how to set up and acquire routine 1D spectra using VnmrJ 2.2D
• WITHOUT using the command line
• WITHOUT manually adjusting the lock channel
• WITHOUT manually adjusting shims
• WITHOUT doing anything sample-specific except for naming the file once the spectrum has been acquired.

The guides itself is just one page and, when folded, fits into your pocket for easy use.

Even if you’re experienced operating Varian spectrometers, you may find something new here that will make your life run more smoothly. And don’t we all want that?

Enjoy!