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Showing posts from July, 2009

QR-DOSY

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At the beginning of the month we saw that there are cases where the diffusion coefficients can be measured with the same mathematical tools used to measure relaxation. We have seen DOSY spectra of pure compounds where each signal decays as a pure exponential. Even a mixture can behave in the same way, if the signals don't overlap. In summary, calculating the diffusion coefficients is often easy. What I was curious to discover was: is it possible to recalculate the components of a mixture if the diffusion coeffients are known? From a pure mathematical point of view the answer was already: "yes", but I wanted to verify it in practice. As far as I know, something like: "QR-DOSY" has never been mentioned. So many DOSY methods already exist and I don't mind to increase the Babel with yet another acronym. Do you? THEORY If we know the diffusion coefficient D(j) we can calculate that the NMR signal in the spectrum i will be proportional to a value A(i,j) = exp(-D(j...

Jacek Stawinski

Q. What's your position and where are you working? A. I am Professor of Organic Chemistry at Stockholm University, Stockholm, Sweden, and at the Institute of Bioorganic Chemistry, Polish Academy of Science, Poznan, Poland. Q. Where have you been working before? A. Adam Mickiewicz University, Poznan, Poland, and Institute of Organic Chemistry, Polish Academy of Science, Warsaw, Poland Q. Briefly describe your research. A. My field of expertise is bioorganic phosphorus chemistry, nucleic acids chemistry, and lipid and phospholipid chemistry ( http://www.organ.su.se/js ). Q. What do you use NMR for? A. Characterization of synthetic intermediates, structure determination, spin simulations, NMR dynamic processes. Q. Which NMR software are you using now? iNMR, the latest version. Q. Which other NMR software have you used in the past? A. Swan NMR, Topspin, MestreC, MNOVA Q. How do you rate iNMR? A. iNMR is superior, by far, to all NMR software I have used. It provides a power...

Bull's-Eyes

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Here are some caffeine peaks (below) and EthoxyEthanol peaks (above). The display is DOSY-like, yet the numerical treatment is a simpler and faster mono-exponential fit. Each column has been processed independently from the rest, and each column yields a different result: Now let's apply a Whittaker Smoother , with a small value of lambda (100), along each ROW: or a big lambda (500): or a huge value (8000): The smoother averages the results obtained from the different columns. The peaks are perfectly aligned.

Wandering

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Jean Marc Nuzillard writes: The example that is provided by Carlos in his blog would benefit from a processing trick I use when there is no multiplet superimposition: I simply integrate the multiplets that are recorded at different gradient intensities and I perform a monoexponential fit on integral values. I suspect the noise on integral values is lower than the one in individual columns of the 1D spectra set, thus making D values more accurate. Bye bye butterflies. This idea is absolutely trivial but maybe it would be interesting to implement it. I agree with the idea. Actually I had arrived at the same conclusion for a different reason. Look at this spectrum (a DOSY after FT): The signal/noise ratio is low yet acceptable, the compound is pure, the decay mono-exponential. No concern about phase and baseline. Alas, this peak is too nasty for my tastes. The frequency is not constant over time. The "trivial" trick by Jean-Marc should work. I give my preference to binning, be...

Pictures

In my fourth year of blogging I have started publishing pictures of spectra. I like my pictures, yet this is not the point. I don't want to convince you that my pictures are beautiful. I want to convince you that I am a spectroscopist and not a programmer. The programmers have always stated that "in the near future" it will be possible to obtain a completely automatic analysis: from the sample directly to the response (meaning a chemical formula or a list of values), by-passing the plotted spectrum. I have found the same concept and expression "near future", scattered in the literature of all the decades, from the 60s onward. I really believe it: someday in the future we'll arrive at the completely automatic analysis. Being that, at this writing time, I am working as a programmer and not as a spectroscopist, I should adhere to this belief and be happy. It happens, instead, that I always think like a spectroscopist scared of remaining unemployed. I really hat...

Ghost of a Butterfly

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Sometimes the butterfly disappears when the picture is scaled down, like into this web page. Click it!

Butterflies

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Carlos kindly gave me a copy of the DOSY spectrum he showed on his blog last year . I am experimenting alternative processing routes. Here is a detail of the caffeine peaks, after applying the rudest (and probably simplest) treatment. The decays have been linearized (by taking the logarithm). The slope of the line is proportional to the diffusion coefficient. The final results are reported as a normal DOSY spectrum. Click on the thumbnail to see the image at natural scale. There is less signal/noise in the tails of the peaks, obviously, therefore the error increases: graphically we see the wings of a butterfly. Being that it's impossible to correct the phase perfectly, some butterflies are asymmetric.