Friday, March 13, 2009

SDBS beautified

The Spectral Database for Organic Compounds is very popular
and deserves all my praise: is straightforward to use, easy to access, rich of data, void of advertisement and completely free. Everybody has used it at least once, what else should I say?
Jaume Farràs Soler sent me a shell script to import a list of peaks, copied from SDBS, into iNMR. He said that the pictures of SDBS were not clear enough, while in this way he could generate much better ones. The address of this script is now:
Later on we'll see why it can be useful. Let's start with a more immediate approach. First thing first: if you have a Mac, download the latest version (3.1.4) of iNMR passion (freeware). Now, the next time you find a 1-H spectrum on SDBS, scroll down the page, until you find this button:Clicking the button leads you to a list like:

  Hz    ppm   Int.

1367.55 3.422 485
1360.72 3.405 942
1353.88 3.388 515
 755.00 1.890 118

Copy the list, including the header: "Hz ppm Int.", into the clipboard. Open iNMR passion and choose, from the menu, "Simulate List of Peaks". You will instantly see the spectrum, synthesized, as large as your monitor, ready to be explored (or printed) and, it goes without saying, anti-aliased.

Caveat: I guess that SDBS reports the apparent eight of the peaks, which is given by the proper height of a peak plus the contribute of any overlapping peaks. iNMR interprets this value, instead, as the natural height. The result is that all the peaks of a multiplet will become taller, while the singlets will be OK.
The areas will be a little distorted. What's also missing from the SDBS list is the width of each peak. In the synthetic spectrum all lines appear equal and narrow (1 Hz wide). The areas of broad peaks will be strongly underestimated. Add to this the effect above (for overlapping peaks).

If you want something more realistic, you can use the script by Jaume. It will generate a list with widths. Import the list into the deconvolution module of iNMR, where you'll be able to modify individual line-widths and intensities. The spectrum will look more realistic, yet don't ask me where to get the correct values from.

If, instead, you know about another database, with a different list format, send me the address. I'll write another version of iNMR passion that will recognize your format too.


Post a Comment

<< Home