Hi @Mazal
Welcome to the forum 
The only way to do so (at least that I am aware of) is to use Python and the according libraries within a Python Scripting node. You can find more information on how to handle chemistry data types between KNIME and Python HERE. There are no out-of-the-box nodes available for this.
Maybe also worth asking in the Cheminformatics Section of the forum, I am unfortunately not an expert in this subject.
Best,
Alice