Chiral centers and adding explicit H atoms
User 25d107bd42
13-01-2008 20:46:12
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.
User 870ab5b546
14-01-2008 02:04:31
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.
User 25d107bd42
14-01-2008 15:31:40
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.
ChemAxon 25dcd765a3
14-01-2008 17:23:15
Hi!
Marvin uses one wedge notation suggested by IUPAC.
So every stereocenter will have only one wedge (if possible).
I also would like to thank Bob for the answer!
Andras
User 25d107bd42
14-01-2008 20:58:20
ChemAxon 25dcd765a3
14-01-2008 21:22:44
We try to follow:
GRAPHICAL REPRESENTATION OF
STEREOCHEMICAL CONFIGURATION
(IUPAC Recommendations 2006)
Prepared for publication by
JONATHAN BRECHER
Pure Appl. Chem., Vol. 78, No. 10, pp. 1897–1970, 2006.
We also try to keep the already fixed wedges and do not rearrange them.
(You can clean wedges if you want to rearrange them.)
In page 1911:
ChemAxon 25dcd765a3
14-01-2008 21:31:17
Moreover if you Clean Wedged bonds.
The wedge will move to the C-H bond, which is the smartest solution.
User 25d107bd42
15-01-2008 19:44:29
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.
User 25d107bd42
15-01-2008 20:00:36
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 ?
ChemAxon 25dcd765a3
15-01-2008 20:17:50
Hi!
I'm convinced.
We will dicuss it and fix this.
Thank you for calling our attention to this.
The asterisk shows the attachment point for the Sgroup.
ChemAxon 909aee4527
17-01-2008 09:02:53
The last post was moved to a new topic:
http://www.chemaxon.com/forum/ftopic3439.html
The first part of the post belongs here:
| Quote: |
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
ChemAxon 25dcd765a3
01-03-2008 14:26:31
Implemented.
The next Marvin release will contain the fix
Thank you for calling our attention to it.
Andras
User 25d107bd42
01-03-2008 22:19:13
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.
Regards, Hans-Ulrich
ChemAxon 25dcd765a3
02-03-2008 08:02:51
The next Marvin release, which is 5.0.2 will contain the fix.
The 5.0.1 has only partly improvement.
Andras
User 25d107bd42
02-03-2008 08:11:57
Can you give me a pre-release, as I got it in another topic? So I will test it.
Hans-Ulrich
ChemAxon 25dcd765a3
03-03-2008 10:47:37
Release of 5.0.2 is scheduled to March 14 (Friday).
Do you still need a pre-release or you can wait until then?
Andras
User 25d107bd42
03-03-2008 13:38:45
Hi Andras,
of course I am always interested in the newest version: It is an offering to test it. It is the second bug fix in this topic.
Hans-Ulrich
ChemAxon 25dcd765a3
03-03-2008 19:58:41
Hi Hans-Ulrich,
Thank you for the offer.
As we are rather busy on this week Tamas will build a pre-release on this Friday.
Andras
ChemAxon 25dcd765a3
07-03-2008 18:17:29
The pre-release is ready.
You can download it from:
http://www.chemaxon.com/test/marvin
We have to fix some bugs related to wiggly bond but the H arrangement should work.
Thank you
Andras
User 25d107bd42
10-03-2008 08:04:31
Hi Andras,
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
ChemAxon 7c2d26e5cf
10-03-2008 12:53:02
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.
User 25d107bd42
10-03-2008 14:39:00
Hi Andras and Tamas,
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) ?
Regards, Hans-Ulrich
ChemAxon 909aee4527
10-03-2008 15:29:13
Hi Hans-Ulrich,
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
ChemAxon 25dcd765a3
10-03-2008 17:54:30
Hi,
Since the built it seems that we've improved.
The current branch produces:
User 25d107bd42
10-03-2008 20:33:02
Hi,
SUPER !
Hans-Ulrich