Automatically assign stereoisomerical information

Hi,

I have some chemical structures without stereoisomerical information (E/Z and R/S). Based on the name of these molecules, I would like to add the missing stereoisomerical information. I wonder if this is possible and if somebody could have an idea how to do that.

To illustrate this, I send you some structures files (mol files), none of them have stereoisomerical information, they are all identical. However 4 stereoisomers are possible:

2R 3R

2S 3S

2S 3R

2R 3S

So do you have a solution to automatically correct these structures based on their names ?

 

Thank you very much for your help.

I am not sure I understand your question. The stereochemical information is specified in these files with the wedges. If you turn the stereo display on (View/Stereo/RS Labels menu), then you will see the corresponding R and S lables displayed. Please see the attached image.

Or do you mean something else on "adding missing stereo information"?

Hi,

Thank you for your reply. I will try to explain myself better: with "adding missing stereo information" I mean that I have a lot of structures files without this information on up/down wedges, and I would like to find a script or a program to automatically do that for a lot of structure files.

So what I actually would like to do is to directly modify the chemical structure in the .mol file.

If you follow this link (http://www.symyx.com/downloads/public/ctfile/ctfile.jsp) and download the document called ctfile.pdf: on page 48 there is a description of the "bond block" and the meaning of values in the bond block. I am interested in modify the "bond stereo" field with the values 1 for up or 6 for down. But I have no idea how to do that, and I wonder if it is possible, and if some of you have done something similar before.

I saw some documentation about the Marvin API, for example the Class TopologyAnalyser (http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/calculations/TopologyAnalyser.html). There are some functions to calculate absolute stereo configuration of a given atom ("stereo") or determines the chiral center atoms ("chiralCenters") ... but is there anything about setting the stereo information?

Thank you for the explanations. You can use the Stereoisomer plugin to generate all tetrahedral and/or double bond stereoisomers of a given structure. Is that what you are looking for?

This is almost what I am looking for !

However I don't want to generate all stereoisomers, but I want to be able to choose which one will be generated. With the example I gave you (the mol file I sent in my first post), there would be 4 stereoisomers possible. But for some other compounds there are a lot more isomers and I don't need them all... So if I want to generate the 2S 3R isomer, I would like to find a function which tells this bond at C2 is S (= down), and this other bond at C3 is R (=up). Is that possible ?

It is possible in two passes. First, you generate all stereoisomers and then filter those, you really need. But how do you imagine filtering? How would you like to specify which confiugurations you need?

Are  you using the API? Then you can call the getStereo(int a) function of the TopologyAnalyserPlugin class to determine the stereo configuration of the given atoms.

So I will try to filter the isomers I want, I think it could work, I don't know yet how I can do this, but I think this is a good solution. Thank you for your help !

Yes, I wanted to ask that as well. How do you know which stereoisomers you want? Do you want to select them manually or you have a kind predefined list  (atom identifiers and their stereo configurations for each molecule)?

Hi,

I have a list of formatted compound names with some information about the isomers after the ";". For example I could have in my list the following compound names:

3,3',4',5,7-Pentahydroxyflavan; (2R,3R)-form

3,3',4',5,7-Pentahydroxyflavan; (2R,3S)-form

etc

Parsing these names I could automatically extract for each molecule the stereoiosmerical configuration required for the different atoms.

 

So my idea would be:

1. parse the names and obtain the stereoisomerical configuration (e.g. "2R, 3R") required for each given molecule;

2. generate all the possible stereoisomers for 3,3',4',5,7-Pentahydroxyflavan;

3. automatically filter within the list of possible stereoisomers the correct configuration obtained from parsing the compound name

The stereo configuration can be part of the compound name. Why do not you just use ChemAxons name tools? Simply paste this into MarvinSketch:

(2R,3R)-3,3',4',5,7-Pentahydroxyflavan

and you will get the compund that you wanted. You can use Name2Structure in batch mode from command line or API as well.

The problem is when I have more complicated compounds, for example glycosides:

- "3,3',4',5,7-Pentahydroxyflavan; (2R,3S)-form, 7-O-a-L-Arabinopyranoside" is the initial name of the compound I want to draw, I don't have the structure for it

- but I have the structure for "3,3',4',5,7-Pentahydroxyflavan; 7-O-a-L-Arabinopyranoside"

- I convert this structure to IUPAC name and obtain: "2-{[2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}oxane-3,4,5-triol"

- I modify the IUPAC name and this gives: "(2R,3S,4R,5S)-{[(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}oxane-3,4,5-triol"

So I have to parse the IUPAC name to know where I should put the R and S? I was afraid it will be to complex, so I was looking for a different approach, just in case. But I will try this IUPAC naming again and hope it will work.

Thanks again for helping me.

Our IUPAC name experts might have an idea, they will respond soon.

Dear Vanessa,

Sugar naming is not supported by us, so a simple reordering of the name and copy-pasting it won't work. I don't know, how many names you have. If you doing it manually you could try to create a strucure from only a part of a name.

So in general i don't have better solution then you wrote. If you generate the stereoisomers and the names of them, you can filter by the name.

Regards,

Rita