Can I define a prochiral centre within a reaction?

Can you confirm that in order to define a chiral centre (i.e. a mixture of enantiomers) in a product I need to assign the chiral atom the "AND1" label?

Prochiral reactions can be defined, but you have to map all neighbouring atoms connected to the prochiral atom. The enhanced stereo flags (Abs, Or, And) will be supported in Reactor with the coming release of the JChem toolkit.

Defining a prochiral/chiral centre, in a reaction context can only be inferred at present, by the surrounding mapped atoms (and presumably the mapping of prochiral to chiral) and is being addressed in the next version(s) - presumably in 3.1, if a prochiral centre is defined in the reactents then potetially 2 distinct enantiomeric products are possible from a prochiral centre, and this will be reflected in the generated output with the chiral atom flagged with it's absolute R/S configuration?

Yes, you can generate chiral products from achiral reactants if you map the surrounding atoms of the stereo centre. Please try the attached reaction (reaction: prochiral_reaction.mrv, reactant: pyruvate.mrv).

Code:

react -r prochiral_reaction.mrv pyruvate.mrv

The next version of reactor will support diastereomer notation by adding ABS, OR, AND flags to the products according to the reaction scheme.