Urgent: How to draw a inorganic formular with Marvin Sketch?

How do I draw a molecular formula which can also be searchable with Marvin Sketch (V5.2.6)?

Please kindly give a detailed description for drawing attached formula as an example. I will save this formula/structure in our database after drawing with Marvin Sketch, in order I can search it later with JChem Base after drawing it in the Marvin Applet.

Looking forward to hearing from you ASAP.

Thank you very much indeed.

Hi,

first it would be good to open a organic chemistry textbook to figure out the correct LEWIS structure, because you were just throwing a molecular formula in. You can search molecular formulas with any text based database. If you want to do a chemical database search you have to draw the structure completely given all connections and bonds. If no textbook is around I usually try to search databases like PubChem and Chemspider. So here you would come across sodium metaborate. You can copy paste the follwing SMILES and you can add water later. The last one is sodium metaborate.

Canonical SMILES:              B(=O)[O-].O.[Na+]
MVIEW SMILES Sodiumboroate:    [Na++][O-]B=O
MVIEW SMILES as ANY BOND:      [Na++]~[#8-]B=O

InChIKey: UYAQHLFAIDLZLE-UHFFFAOYSA-N

InChIKey= ATQYHYQAFNMFBB-UHFFFAOYSA-N

 

or you can draw it like this (the dotted bond is any bond and the oxygen has a negative charge):

 

In order to find the correct conformers, you need to go to a database like CrystalEye Database or you can do a direct calculation with the MARVIN forcefield. See below:

 

Cheers

Tobias

Thanks for your instruction for darwing the inorgnic structure with Marvin sketch. However, how I can add the number of water of crystallization during drawing, such as below formula:

NaBO₂•4 H₂O

In addition, after drawing the structure in Marvin applet like you introduced, the formula was automatically generated in a radom arrangements for the elements, please kindly find the attachment for a screen-shot.

The formula I expect to see is NaBO2•H2O, not BH2NaO3. Alternatively, NaBO2 is still ok if there is no water of crystallization drawn, not BNaO2. How can I get this kind of formula?

Thanks for your help.

Hi,

1) by creating a dot-disconnected formula and parsing it?

Dot-disconnected formula = H2O.H2O.H2O.H2O.BO.Na

O.O.O.O.[Na+].[O-]B=O

[#8].[#8].[#8].[#8].[Na+].[#8-]B=O

I think its best to store in MRV format or just write a small MVIEW extension using the API.

You can use the group feature see here:

 

 

2) "NaBO2 is still ok if there is no water of
crystallization drawn, not BNaO2."

Have you heard of the Hill system?

3) BNaO2.H2O or BNaO2.[H2O]4 or BNaO2.(H2O)4 is that OK?

Could be a feature I guess if you ask?

See graphic below, a crystal water formual structure?

Yes its shopped, but I guess it can be easily implemented in this way.

Cheers

Tobias

Hi,

Thank you Tobias for you responses here. Yes, presently I cannot think of any better solution with Marvin either.

Yuming, the structure has to be drawn correctly, otherwise the searches will give you incorrect results. Then, I think, you should write a small program in your custom application that uses the information given in the dot disconnected formula, and converts it to the form you want to display.

Best regards,

Akos