ANYStructures - undefined Structures

Hi all,

I'm searching for a possibility to work with "unsure structures" in a database.
We want to store structures of impurities, that cannot be defined exactly. We know parts of the structure, and we know the composition (formula) and we want to store the information we know about these structure. As we want to compare the observed exact mass of the impurity with the calculated mass of the structure we need the ability to calculate the formula and the exact mass of the stored "unsure structure"

So I was really happy to see the "any structures" structure type when creating a new database table in IJC.

The formula and the exact mass is interpreted correctly even when I use abbreviation groups like "C10H21" (see attached screenshot). And we can work with position variation bonds.

But what we also need is an ability to add not predefined formulas like "C10H16N3O2".
So we could store the part of the structure we know as well as the part of the structure we just know the formula in an "any structure" field in the database.

Does anybody see a possibility ?

Thanks in advance

Udo

Hi Udo,

 

Selecting ANY structure is a good choice, you can populate this DB with any structure drawn with no limitations.

I am not sure what is your demand exactly.

In case if you are thinking about splitting the molecule into known and unknown fragments; you are able to draw these fragments just simply next to each other on the canvas (without defining any bond between them). However, please note, that you can not calculate molecular properties (e.g. mass) just for a fragment, but for all the structures present on the canvas (all together).

An other solution would be to draw Markush structures where you have a plethora of possibilities for defining known and unknown parts of your molecule. A lot of information could be read here: http://www.chemaxon.com/products/markush-ip/ where you may find also links to different guides (documentation) too.

 

On the other hand you can add new/custom columns to the already existing DB in which you can insert any arbitrary data.

 

I hope I could give you some hints. 

Please, do not hesitate to reply in case I misunderstood you question or some clarification would help you.

 

Best regards,

Norbert

Hi Norbert,

Thank you for the fast reply.

I think, my sentence "we could store the part of the structure we know as well as the part of the structure we just know the formula in an "any structure" field in the database" was a little bit confusing - sorry about that.

We just want to store one "any structure".
From a part of these structure we know the exact structure, but from a part of the structure we just know the formula (like C8H16ClNO2 in the attached example).

I have seen the function "Insert Groups ..." in Marvin Sketch, but there I need to define a structure of this group before I use it.

In our case, we do not know a structure of the "group C8H16ClNO2" we want to connect with the known structure part. So we would need a function like "Insert Formula ..." or something like that.

Maybe there is still a way, or a workaround to create such a structure. I would be happy if YES.
In the Markush-Guide http://www.chemaxon.com/products/markush-ip/  I didn't find a soulution

Thanks,
Udo

Hi Norbert,

Another Idea was to use the "Periodic Table and More" Tab to add a Formula as a Pseudo atom.
This leads optically exactly to the structure I want to store in the database.
The only problem is, that the Formula and masses cannot be calculated.

Do you see a possibility to enable JChem to calculate formulas and masses of this kind of structures?
Or is there another way to create a structure, where the calculations work?

Thanks
Udo

Hi Udo,

 

Now I see what do you meant.

Unfortunately I don't really now a very easy way of doing so (e.g. attaching just a formula to the structure). A way that could work is to use user defined abbreviated groups (Superatom group) for all the "formula". This could get painful if you are having a whale of formulas that need to be defined before its usage.

About Abbreviated groups you can learn reading this link: https://www.chemaxon.com/marvin/help/sketch/sketch-chem.html#sgroups

 

I move this thread to the marving guys, they might have some better idea how to solve your problem.

 

Best regards,

Norbert