About T (Tritium), D (Deuterium)

About T (Tritium), D (Deuterium)





Because T (Tritium), D (Deuterium) could be used in MOL file,


I would like to know whether Standardizer support T,D.


(I know SMARTS uses [3H], [2H] to display T (Tritium), D (Deuterium).)





I tried the following transformation. But it failed.


<Reaction ID="TEST_A" Structure="

[3H]>>

[T]" />


Do you have any ideas or workarounds?





Best Regards

No, D and T is not supported at the moment, but you can use [2H] and [3H] instead, as you mentioned.


Do you have many structures with T and D?

One of our customers requested some workarounds.


If there were not any, I would like to know it is possible to let standardizer support T, D in the next version.





The customer have some MOL files with T,D.


I would appreciate your any suggestion.

Marvin imports molfiles containing T and D atoms with no problems, however they are automatically displayed as [2H] and [3H]. So the compounds remain chemically the same, just the representations of these two isotopes are differents.


You would not like them converted, would you?

If possible, I would like they are displayed as T,D after the conversion.

It seems, that this is not just a display issue. If I know well, D and T are pseudo atoms and not they do not match [2H] or [3H] in MDL software?





As a solution we can probably import D and T as [2H] and [3H] with atom aliases 'D' and 'T'. This way D and T is displayed while we maintain the correct hydrogen isotope meaning. What do you think?





SMARTS export of D would be difficult, since D is a means something different in SMARTS (number of explicit connections).

Marvin 4.1 will display T and D for molecules originated from molfiles containing T or D atoms. These will be the correct isotopes with alias strings.