Various questions about template and drawing

Hi,

First question : I'm interested in using an C70 fullerene structure, but it doesn't exist among the aromatic templates. I only found C60, C80 and C100. Is it possible to get it using a community library for example? is there a place were user would be able to get "more" templates ?

 

Second question : Is there a possibility to duplicate a molecule in a marvinsketch window ? I don't find the way to do this and it's something that would help me when I need to draw various modifications of macromolecular system. "Copy" and "Paste" shortcut don't work.

 

Third question : what is the way to turn "-CH3" group as implicit group ? I explain myself : When I draw chemical structures, the final methyl group (for example) is always explicit. Sometimes I would like to view only the bond and for the moment I don't find the way to do this. It's probably obvious, could someone help me ?

 

That's all... for the moment. I hope that I explain myself correctly, my english is not perfect.

Thank you for answering.

I forgot to give the following information : Academic Package Licence / MarvinSketch 5.3.01 / Mac OS X (version 10.6.4)

Dear Mathilde,

 

1. Currently we do not have the C70 template in our template library, but you can find C70 in e.g. PubChem, and then if you copy e.g. the InChI to Marvin:

InChI=1S/C70/c1-2-22-5-6-24-13-14-26-11-9-23-4-3(21(1)51-52(22)54(24)55(26)53(23)51)33-31(1)61-35-7-8-27-15-16-29-19-20-30-18-17-28-12-10(25(7)56-57(27)59(29)60(30)58(28)56)37(35)63(33)65-36(4)40(9)67(44(17)42(12)65)69-46(11)47(14)70(50(20)49(18)69)68-43(13)39(6)66(45(16)48(19)68)64-34(5)32(2)62(61)38(8)41(15)64

then select Structure > Clean 3D > Clean in 3D, you will have its proper stucture.

 

2. Copy/paste should duplicate the structure; please try again, it should work.

 

3. View > Implicit Hydrogens > Off

 

I hope these answers help. Best regards,

 

Akos

Good day, 

I intend to draw some fullerene type molecules and wonder if it is possible to do that using Marvin Sketch MarvinSketch 5.5.0.0 / Mac OS X (version 10.6.8).

The molecules are C₈₂ and Gd@C_82.

Thank you in advance.

Dear Pearly,

 

I think the easiest solution is not drawing but the import these huge molecules.

You can start  for example here: http://www.nanotube.msu.edu/fullerene/fullerene-isomers.html.

(Please note that after importing you have to select the whole molecule and change all bonds to aromatic ones.)

Please find attached the .mrv file containing one C82 isomer, obtained by the above method.

If you require any further assistance, please do not hesitate to contact us.

Kind regards,

Nikolett Mihala

Dear Nikolett Mihala,

Thank you for your reply. 

When you mean importing the file, you mean taking the xyz coordinate? 

From there, I just change it to the aromatic form, right? The structure looks a little strange, actually. Maybe I did it wrongly (picture attached).

Another question is that, how do I transform the structure into a metal fullerene?Can I just insert the metal atom into the structure?

Sorry for the many questions.

Dear Pearly,

 

You can import the.xyz files from the above mentioned source.

Clicking on the image, a dialog box appears, where you can open the file with a choosen application ie. Marvinsketch (MarvinView is the default) or save it and open from the File Menu of MarvinSketch.

Once the molecule is on the canvas with a selection tool or the hotkey select the whole structure and change the bond type to Aromatic (Tools toolbar<Bonds<Aromatic).

To change the display of the aromatic bond  from select Convert to Kekule option from Structure<Aromatic form menu. (I think you find the image weird because the Aromatic display is your default,  and not the Kekule method).

To add a metal you can use coordinates bond (Tools toolbar<Bonds<Coordinates) or if you prefer you can opt for the graphical solution.

Of course, you can find other online sources with different file formats.

I hope this helps, but if you have any further questions please feel free to contact us.

Kind regards,

Nikolett Mihala