I was wondering about how to specify formal charges in molecules, particularly zwitterions. When I create a molecule using an xyz-file (see attached), this charge separation isn’t included since the molecule’s total charge is zero and only atom positions are encoded in the file. To my understanding, this means that Psi4 interprets this as two radicals (see attached image). Or am I off track since formal charges (as the name suggests) are a formality, and I should let Psi4 figure out the physical charge distribution from the atom positions and molecular charge alone?
Thanks and best,
phenolate_zwitterion.xyz (605 Bytes)