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Issues with C-H bond lengths
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Hans-Ulrich

Joined: 24 Oct 2007
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Link to postPosted: Tue May 01, 2012 9:14 pmPost subject: Issues with C-H bond lengths Reply with quote

Hi, I am still looking for a tool to produce reasonable coordinates for planar molecules. The molecules should be in the xy-plane and the bond lengths should have reasonable values. Our quantum chemical programs analyse the topology of the molecules by searching for neighbors in a range of normal experimental bond lengths. The molecules MarvinSketch produces have normally those tolerable bond lengths, but the C-H bond lenghts have 1.54 A. This is much too long.

In the attached image there is shown, the tool Add Explicit Hydrogens produces all C-H bond lengths as 1.54 A (the same length is produced for O-H and N-H bonds, being also too long).

Using Clean 3D with Hydrogenize produces reasonable bond lengths. But now the molecule is not in the xy-plane. So using now Clean 2D brings it back to this plane, but it changes once more the bond lengths and the C-H bonds have 1.09 A. This value is a good reasonable C-H bond length. But now the problems checker says "6 bonds found with wrong length".

Saving this structure as xyz-file gives a structure having CC 1.54 and CH 1.09 values for the bond lengths. And these structures are usable.

But using Clean 2D once more a second time now changes the C-H bond lengths to 1.54 A.

So there are at least two problems to be solved:

1) The failure in the problem checker showing reasonable bond lengths as wrong.

2) The much too long C-H and N-H and O-H bond lengths Clean 2D is producing.

Best regards, Hans-Ulrich

PS: This is not the first time I am discussing the C-H bond length problem in this forum. And one of our programs has been adapted to C-H bond lengths having 1.54 A. But we cannot do this for all programs.

PS2: Please remember: We would like to use Marvin for teaching.




 Filename: Fulvene-Bondlengths-2.png    Filesize: 140.72 KB    Viewed: 7029 Time(s)
 Description:  C-H bond lengths
Fulvene-Bondlengths-2.png
Peter
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Link to postPosted: Wed May 02, 2012 1:13 pmPost subject: Reply with quote

Hi,

 

We can introduce a 2D cleaning option which sets the X-H bond length to 1.0. The default behaviour will be that all the bonds have the same lengths in 2D. It's a sketch of a molecule not the actual structire and other users like this representation more. 

Will be this ok for you?

Thanks for the report, we've found an other bug in Clean2D too.

 

Regards,

Peter

Hans-Ulrich

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Link to postPosted: Wed May 02, 2012 1:58 pmPost subject: Reply with quote

Hi Peter, thank you for your very fast answer.

It would be fine to have the option to get reasonable X-H bond lengths.

But I don't believe "other users like the long X-H bond lengths more".

Anyway, MarvinSketch is already using the default 1.09 as shown in the first Clean 2D in my fulvene image example above. But as shown in my image documentation using once more a second Clean 2D with the same molecule changes C-H to 1.54 . Why ?

What's about the problem checker ?

Best regards, Hans-Ulrich.

PS: Clicking on the link in the email I don't see the attached image. I must first log in and then I can see the images. But newcomers and other forum visitors cannot see attached images at all. I have already complained this problem in another post. But now I will start a new topic to discuss this defect.

PS2: And what was the second bug. As a programmer I would like to hear about it . You may inform me using email.

Peter
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Link to postPosted: Wed May 02, 2012 2:44 pmPost subject: Reply with quote

Hi, 

 

The second bug is that the first time Clean2D is called on a molecule that was cleaned in 3D, the C-H bond lengths stayed the same. 

I've tried several other sketching programs (ISIS/Symyx/ChemDraw), and all of them used the same bond length to C-H bonds. I think it's because In 2D the chemical "position" of the atoms are more important than the drawn position, because in reality molecules are 3D objects. (except for planar molecules of course)  

I will ask my colleague about BondLengthChecker.

Regards,/p>

Peter

Hans-Ulrich

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Link to postPosted: Wed May 02, 2012 3:18 pmPost subject: Reply with quote

Hi, I cannot agree.

Please look at my documentation image. The first Clean 2D changes the C-H bond lengths from 0.99 to 1.09. And this is not a bug. It is at present the only workaround for us to get reasonable structures. Please do not destroy this possibility.

Let me repeat my sentences: Saving this structure as xyz-file gives a structure having CC 1.54 and CH 1.09 values for the bond lengths. And these structures are usable.

And I still don't believe "In 2D the chemical "position" of the atoms are more important than the drawn position". Why should the H atoms having only one bond not to be nearer to their neighbors ? So the positions are clearer as otherwise. But this is not really important for us. More important is to have the workaround described before.

If you destroy the first Clean 2D procedure we have no way to get better start geometries.

Regards, Hans-Ulrich


Peter
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Link to postPosted: Wed May 02, 2012 6:00 pmPost subject: Reply with quote

Hi, 

We won't fix the other bug until we provide the option to shorten C-H bonds. Sorry for not telling this earlier. I understand that this workaround is important for you.

Regards, 

Peter

Peter
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Link to postPosted: Thu Jul 19, 2012 10:16 amPost subject: Reply with quote

Hi, 

 

I'd like to inform you that in 5.10.1 we've introduced a new cleaning option in clean 2d: -s. It shorten the H bond legths to 1.00.

http://www.chemaxon.com/marvin/help/sci/cleanoptions.html#2d

You can make Sketch use the clean with this option by inserting the following line to HOME/chemaxon/marvin.properties


clean2dOpts=s

We're planning a menu option for this, but it's not ready yet.

Regards, 

Peter

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