Friday, December 01, 2006

JSpecView Demo

Original Post

Jean-Claude Bradley: So I’d been meaning for a little while to do a screen cast to show why it is so useful to use JCAMP, and specifically JSpecView, to look at your NMR spectrum. Here’s an example on Experiment 42, which is an experiment that was done recently by MI grad student, Khalid. This is on the UsefulChem wiki. And it involves basically mixing phenylacetaldehyde with t-butylamine, trying to monitor the formation of the resulting imine. Now, what makes using JCAMP so useful is that you don’t have to take a whole bunch of expansions to get the information that you need from the spectrum.

Let’s take a look at this phenylacetaldehyde, for example. We basically just have a single file on HTML, and when we click on it you see that the spectrum pops up in a little applet, and we can do a lot of things to this without needing to look at different printouts. For example, if I look at the aldehyde peak, I simply have to left click, drag, and where I want to stop I can see that this expansion happens.

So I can expand the spectrum all the way to see that triplet very clearly and be able to take differences between the peak positions to get JCONSTANTS [sp] for example.

Now, if we go back to the original spectrum, we’re going to clear all the views, we can also do integration. So to do the integration on JSpecView we right click, we view and then integrate, and we can modify these factors to make it look prettier, but let’s just use the defaults. And we see this yellow integration line. Now again, we can extend any area that we want. So if we looked at the CH2 [sp] group for example, this is phenylacetaldehyde that we’re looking at, we can expand it, we can see that the integration can be calculated pretty easily. On the top right corner there are two numbers that are giving you your position at all times with the cursor. So if we look at the top of the integration we’re looking at roughly 125, right? And underneath is 105. So we’re looking at about 20 units for two hydrogens, OK?

So now we will zoom back, clear all the views, and we’re going to expand the aromatic region. And again we can subtract the two numbers, so disintegration ends at about 105 and starts at about 55. So we have 50 units for five hydrogens. Again, we have about 10 units for hydrogen.

We’ll zone back, clear all the views, and look at the aldehyde area. So now this one has about 54 minus 48, so we’re looking at six units is supposedly representing one hydrogen. So there is a problem with the integration on this spectrum and I am putting this up as a question out there to try to see if anybody can actually answer me as to why we’re having an integration discrepancy with this spectrum.

So this brings up another really useful aspect of JCAMP in that all of the parameters of the NMR experiment are automatically recorded. So in JSpecView, to see that, we right click and then we look at view, show header, and we can see all the parameters here. So we can see that it was done on a 300 MHz machine. We can look at any number of scans and just everything that was done for these experiments.

So now we can monitor what happens when we mix phenylacetaldehyde with.

T-butylamine, so we’ll go back. And there are a number of spectra here. If you look at the logbook, most of them have already been linked, but we’ll just take a look at the very first five minutes after mixing.

So again, we click on this link, and we have in JCAMP format, so let’s take a look at some of the new peaks that are coming out after five minutes of mixing the aldehyde and the imine. Well, we still have our aldehyde, our original aldehyde triplets. Zoom back out. And we can see in this aromatic region, a little bit down still from there, we have a few more peaks that are popping up, and I want to focus specifically on this little triplet here that’s coming up.

So if I magnify this, I can see that it’s coming in at about 7.65, and I can measure the coupling constants, which is 5.3 Hz in this case. I can then zoom out, all right? Because I’m thinking that that triplets may be the imine proton that will be coupling with the ECH2 [sp] group. So if we look elsewhere in the spectrum, a little bit more up field, we see that we have another little doublet that’s popping up, and this doublet is around 3.57. And again, if we calculate the JCONSTANT [sp] for this doublet it’s 5.3 Hz, and so there is a good likelihood that those two peaks are representing our imine that we’re trying to form.

Let’s click back to take a look at the molecule that we’re talking about. So we’re talking about the imine of phenylacetaldehyde and t-butylamine. So it turns out that this reaction actually does not end up being clean. If we take a look at what happens after 42 minutes we see that there is in fact a lot of stuff coming in besides the imine, especially if you look if we look at this region between two and six roughly. There are all kinds of other peaks coming in. Maybe these are related to some elbow [sp] condensations that are happening, but the bottomline is that this reaction is really difficult to do directly like this.

So hopefully I’ve demonstrated with this little example just how useful it is to keep your spectra in JCAMP format, and I’ve got to have to thank Robert Lancashire for developing JSpecView to enable us to do this. These spectra were very easily converted from their original format on our Varian 300 MHz instrument, and we actually have a little tutorial on how to do that. If you go to the UsefulChem site, click on the contents page, you’ll see instructions here for saving in JCAMP format on the 300 MHz machine, for example, and that should enable you to do the same thing so you don’t have to spend a lot of time printing out expansions for regions that you’re not sure that you want and need. Just post your file online and let people at it.


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