NMR prediction

Here is another pretty cool tool, prediction of ¹H NMR spectra.

This is the spectrum of the substance from last post as predicted there. It looks kind of like the real one and none of the shifts are off more than .5 ppm.

The original author's homepage has a better design but the second plugin is not working in my browser.

Generating structures

I just heard of a pretty cool tool for generating structures.

Imagine the following problem. You have the structural formula of some molecule, let's say

And now you are wondering what the molecule actually looks like. If you have a "real" molecule model kit, you could use that. But you probably don't carry that around with you everywhere, it may not have enough atoms and it does not give you quantitative information and so on. The alternative is the Online SMILES Translator.

First you draw your molecule in a standard molecular editor (e.g. ChemSketch) and save it as a .mol file. Then you upload it to that tool and create a 3D mol file. Open the result in a 3D molecular editor: for example Pymol if you want nice pictures; Arguslab if you want some quantitative information and do computations.

The structure I just mentioned looks like this.

I did not really find any special information in this case. But for example it is interesting to notice that the part of the ring with the double bonds is planar.


The side remark is that there are of course more interesting things than just the global minimum (assuming that the tool even finds this minimum). For example other stable structures and the barriers to get a feeling of the dynamics. But I think it's still quite a bit of information for how fast it is and for how little input it needs.

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Add on: At this site you can use the CORINA structure generating tool without the need of any other software. "Create molecule" opens a java applet editor, the result is shown in another applet, both in your webbrowser.

tRNA

It's about time for some more pictures. I picked tRNA because of a course about modelling nucleic acids which I am doing these days.

The secondary structure looks like this, the clover leaf. The amino acid is bound at the top, the anticodon at the bottom. The lines represent the base pairing.


For the 3D structure you have to first consider that helices are formed with base pairing - twist around all those parts. In tRNA there is an important tertiary element, the connection between the left and right loop - fold the molecule. You will get something like this.


The open end is shown in read, the anticodon green, the right loop yellow, the left loop cyan.

Twisted around:

The open end:

The anticodon loop:


These three bases are probably the anticodon. They are GAA which correctly codes for Phe which this piece of tRNA is supposed to do.


If you want to move the molecule yourself you can find the link to a jmol applet from the pdb.