Post subject: Chiral centers and adding explicit H atoms
Posted: Sun Jan 13, 2008 9:46 pm
When doing the following:
1) Insert-Template-Amino Acids-L-Isoleucin -> upper formula in the screenshot
2) Edit-Add-Explicit H Atoms -> lower formula in the screenshot
The carboxy-group at C2 is going from the upside wedge downside. Why?
What has happened at C2? Where are the three groups which are bonded with a line to C2, above or below the drawing plane?
The configuration is still the same 2S-3S and it can be seen in the MarvinView window. OK.
I think the new H atom should be always added on the side as the wedge bond is bonded (see the red points at C2 in the upper formula and the green points at C3). Or describing it in another way: The new H atom should be added at the obtuse side of the C3-C2-N angle which lies in the drawing plane. At C3 it is done this way, and the wedge bond does not change.
Marvin looks around the C atom and puts the H atom in the roomiest location available. Because the roomiest location in your drawing's case points opposite to the wedge bond, it needs to invert the direction of the wedge to retain the absolute configuration. If it worked as you suggested, your structure might end up with some H atoms sitting on top of each other, rather than nicely spread out.
I mean, adding a bond to a chiral center (having a wedge bond) with a new line bond doesn't make sense. Where are now the three groups connected with a line bond ? See the screenshot left L-alanin molecule.
The fourth bond to a chiral center *must* be added by a new wedge bond, opposite to the other wedge bond. See the screenshot right L-alanin molecule.
I must repeat the two last sentences of the IUPAC paper you have posted above: "Since in this style the drawing implies that the central atom is coplanar with substituents A, B, and C, it is technically incorrect in the strictest sense. In preference it should only be used for cases where the central atom is in a fused or bridged ring system." So it is unusable for these amino acid chain systems.
In the meantime I got the IUPAC paper you are mentioning above from our faculty library. The paper is very interesting and has many good examples.
And I found in it the formulas in the appended screenshot. So amino acids should not be drawn with only one wedge bond.
One more post. I have installed now Marvin 5.0.0. I like it and I will now test the nice new features.
I used the "Clean Wedge Bonds" tool you are mentioning above (to the alanine molecule shown above). The S-configuration is now better to see, but I think this does not solve the problem to have only one wedge bond at a chiral chain center, see screenshot.
By the way: What does the little asterisk near the N-Atom mean ?
Hi, thank you for your posts.
It is really a good forum to discuss problems. And the software to post a subject is well programmed. To have bold, color and all the other options is a nice feature. To add attachement in a comfortable procedure is fine. And the best feature is the "preview" option.
Judit
volfi
Joined: 07 Jun 2004
Posts: 283
ChemAxon personnel
Hi,
I just downloaded the newest version 5.0.1 and tested the option "Add explicit hydrogens" using three template amino acids, see the screenshot going down from window (1) to window (2).
The formulas shown in window (2) are still "not acceptable" using the designation given in the IUPAC Recommendations 2006 page 1914.
Acceptable formulas are shown in window (3). It is done in the way, I have mentioned in my first post in this topic (see above red and green points). The wedge bonds must be on the same side of the bonds in the drawing plane. And one must be solid wedged and the other hashed wedged.
sorry, I cannot find the download link. I am only leaded to the "normal" download pages, or back to the home page. And on the page .../test/archives there is no pre-release 5.0.2pre-release.
Hans-Ulrich
Tamas
Joined: 21 May 2004
Posts: 1264
ChemAxon personnel
Select any link in the upper part of the download page (they refer to the mentioned downloadables of 5.0.2pre2.
Probably, you have choosen the "devel" link that refers to the alpha releases from the upcoming Marvin 5.1. Currently, there is not any accessible download alpha from this major release. That's why you have not found anything in that directory.
OK. I found it, downloaded it and tested it. (You should look at my "Desktop", there are now 6 versions ;-)
The test looks good for the amino acid templates which come with Marvin,
see screenshot392. All new H-atoms are added from the correct side and in the correct configuration.
But adding H-atoms to our templates in the NCC-formulas (see another topic from me) on problem is in threonine, see screenshot393. At C-3 the "downwedge-hydrogen" is cut and the OH-group is going up ?
BTW: What is the purpose of the new button Structure - Add - Absolute Stereo (CHIRAL) ?
regarding the Structure - Add - Absolute Stereo (CHIRAL) button:
the function was already available, we just included a new icon image so that it can be added to any toolbar with customization.
These are the new icons in 5.0.2:
Clean2D, Clean3D, Reset View, Insert IUPAC Name, Add/Remove Explicit Hydrogens, Aromatize, Dearomatize and Add/Remove Absolute Stereo.
If you frequently use one of these functions, it's worth adding it to a toolbar.
Kind regards,
Judit
volfi
Joined: 07 Jun 2004
Posts: 283
ChemAxon personnel
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