Feb 042013

I got a new toy. It came in a very large crate.

If we can’t use a forklift we’ll have to use a crane.


Here we see the crane paying for my cardiologist’s kids to go to college as it lifts the magnet over the building…

…and then lowers it through the roof hatch into the magnet room.

Wolfgang is very excited, since he has been working for several years trying to get this magnet to Brown.

And here’s Bruker’s technician Joerg getting started on final assembly.

The 500 struggles with feelings of inadequacy. Don’t worry little magnet, we still need you!

Apr 232008
Our 500, that is. As I related in previous posts, our 500 MHz spectrometer was hamstrung by the signal from a local HDTV broadcast and subsequently had to be moved to a space in the basement of one of our research buildings. This process took about a year, because that space first had to be renovated, and in fact the last upgrades to the space won’t be finished for several days yet. But the 500 has moved into its new digs, (hopefully) finished quenching, and is ready to work. So yesterday I finally was able to collect an HSQC on it for the first time in many months.

So, here’s the spectrum I got:

For comparison, here is the last HSQC taken before we stopped using it. Obviously, this is of a different protein, but both spectra were taken using the same probe on samples with the same concentration, at the same temperature. I countoured them identically. The only difference here is that the protein in the spectrum below has much better relaxation characteristics than that in the spectrum above. In theory, this should produce much better signal to noise. Oh, and also that when I took this spectrum I was also receiving data about cubic zirconium.

This is really good news for a couple of reasons. The first is simply that we have another magnet, and that allows us more flexibility in scheduling. No more fighting when people want 9 days of NMR time next week. The second thing is that, for a variety of reasons, some experiments just work better on a lower-field magnet. In particular, I have some experiments that are sensitive to chemical shift anisotropy and REX; using a lower-field magnet attenuates both these problems.

To learn NMR…

 books, nmr  Comments Off on To learn NMR…
Aug 212007
I picked up James Keeler’s Understanding NMR Spectroscopy because of a teaching dilemma. Students who come to an NMR lab often want to “learn NMR”, though of course this is not really possible in a 2-3 month rotation. They can at least get started in NMR, but in order to do this effectively they need a resource to study and discuss with whomever has charge of them in the lab. I’ve had trouble finding an appropriate book for this task. High-Resolution NMR Techniques in Organic Chemistry, originally by Derome and now reincarnated by Claridge, is a fine introduction for general NMR study but is not at all oriented towards biomolecules and relies heavily on the vector representation that doesn’t always help a student understand techniques such as HMQC or HSQC. Protein NMR Spectroscopy, by Cavanagh, Fairbrother, Palmer, and Skelton is an excellent resource for the advanced student, and has just come out with the long-awaited new edition, but the pages of mathematics and occasionally obscure language are really too intimidating for beginners.

Understanding NMR Spectroscopy is, I think, the resolution of this dilemma. Keeler’s text is clear, describing the physical basis of NMR in a straightforward way that should work for just about any student. He handles the necessary quantum mechanics and operator representations with a deft touch that makes their mathematical derivations clear without producing an intimidating morass of equations. Naturally, some detail and rigor is swept under the rug in this approach, and an advancing student will want the Cavanagh book or Levitt’s Spin Dynamics to get a firmer grasp of the nuts and bolts, but as an introduction to the theoretical underpinnings Understanding NMR Spectroscopy is superb. Keeler’s explanation of relaxation processes is also excellent, and includes perhaps the best physical description of T2 relaxation I have ever read. The book also includes a useful little chapter on the workings of an NMR spectrometer that, while nothing special on its own, is also a good resource for an early-career grad student or rotator. Exercises at the end of each chapter can also be a good teaching tool (although, since the answers are available at spectroscopyNOW, not appropriate for a course).

Although the book is not explicitly oriented towards biomolecular NMR, it has a strong focus on heteronuclear experiments that ensures the information presented is appropriate for students interested in biomolecules.

I can’t praise this book without reservation, however. Some topics that might be considered important are glossed over or skipped entirely — chemical exchange, for example is barely mentioned, and REX not at all. Residual dipolar couplings are not discussed, and the angular dependence of the dipolar interaction is only skimmed. Chapters 10 and 11 are poorly structured and include inadequate and possibly confusing discussions of raising and lowering operators, coherence order, and coherence transfer pathways and diagrams. The mentor will need to take an active hand in explaining just what is going on in these sections.

That said, I think that Understanding NMR Spectroscopy will be an excellent book for grad students just starting out in biomolecular NMR or possibly rotating students who want a glimpse of the nuts and bolts of NMR theory. The gap between Derome/Claridge and Cavanagh has been pretty neatly filled by this affordable little volume ($40 at Amazon).


 boo, equipment problem, nmr  Comments Off on HDTV
Aug 142007
This story begins back in March, when I got an amazingly crappy hetNOE spectrum from our 500 MHz spectrometer. The hetNOE is always a low-sensitivity spectrum, but for a 1 mM sample the signal I got was simply unacceptable. At first, I didn’t think much of this, for the simple reason that I thought the HX probe was in, and I’m used to getting poor signal-to-noise from that thing.

Except… except that everyone else was getting low-quality spectra too, no matter what probe was in. Finally one day Chris and Janice got almost no signal at all from an HSQC of a 1 mM monomeric protein, and that was the end. We had Sara test the magnet, and she found we had a four-fold reduction in signal to noise. To put things into perspective, we would have to take 16 times as many scans as before in order to achieve the same signal under these conditions. For a 1-hour HSQC, this is marginally acceptable. For a 2-day triple-resonance sequence, it is not. The new noise, strangely enough, came and went at odd times.

Al, because he knows all, immediately suspected a television signal, which he attributed to a rogue broadcaster somewhere out on Bear Hill. You see, an NMR spectrometer is really two things. It is a giant magnet, yes. But it is also a radiofrequency transmitter and receiver. The RF pulses induce a signal that the transmitter/receiver coil picks up. For our 500 MHz spectrometer, the primary signal we pick up is the proton signal at 499.75 MHz. This frequency is in a TV band.

Al was deflated, however, when Wlad tried to check the spectral band on his TV and found nothing. The search for the cause continued, with suspects ranging from the Brandeis student radio station to the construction crew radios to various parts of the magnet to secret government transmissions.

In the end, Al turned out to be right, and Wlad turned out to have a cheap TV. There was a channel broadcasting in this frequency range, but it was HDTV channel 18, a signal Wlad’s cheap TV cannot decode. Our spectrometer can’t decode it either, but we can sure see it. It knocks our signal down to an unrecoverable level. You can lose 75% of your signal for a small molecule and still be OK, but with proteins it’s a different story. The spectrometer is essentially useless to us in this condition.

And the worst part, the very worst part about this is that it’s a terrible channel! WMFP digital channel 18, broadcasting in the 494-500 MHz band, airs infomercials and “Gems TV”! Yes, that’s right, our scientific research has been derailed by a display of cubic zirconium jewelry in glorious high definition. Their antenna is located just south of us and we’re right in one of their strongest broadcast regions. Natural cures and cash-at-closing real estate ads are screwing us badly.

Hopefully, we’ll be able to boost the spectrometer’s frequency out of the channel 18 broadcast band to something like 500.13 MHz. However, there’s a Channel 19 (WGBH) broadcasting in the 500-506 MHz band as well; the spectrum analyzer shows a little gap between them that we can hopefully hit, and the WGBH signal is only half as strong as WMFP. Still, we may be screwed even if we boost the frequency. And there’s no way to shield the magnet, except maybe in the basement, but we’ll need to renovate the basement area in order to do that. So basically, we are screwed.