For anyone who is interested and might have the same problem

The solution looks like this:

\begin{document}
\font\up="Linux Libertine O:+sups,script=latn,language=DEU"
\font\down="Linux Libertine O:+sinf,script=latn,language=DEU"

\ce{^{\down 14}_{\up 6}C}
\end{document}

That produces the desired output.

BUT: This just has to be an utter hack and I can not believe it is the way it 
is supposed to be done.
I'm putting the scientific inferior numbers in the upper position, and the 
scientific superiors in the lower position. Does that make sense to anyone?

Cheers
Sebastian


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