Molecular
dopants such as 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane
(F4TCNQ) can interact with conjugated polymers such as
poly(3-hexylthiophene-2,5-diyl) (P3HT) in two different ways: they
can undergo integer charge transfer (ICT) or they can form a partial-charge-transfer
complex (CTC). Both are seen experimentally, but the CTC has been
challenging to characterize, making it difficult to answer questions
such as the following. Which polymorph is more stable? Do they have
similar barriers for formation? Is there a thermodynamic route to
convert one to the other? Here, we study the structure and the thermodynamics
of bulk F4TCNQ-doped P3HT with all-atom molecular dynamics
simulations, using thermodynamic integration to calculate the relative
free energies. We find that the ICT and CTC polymorphs have similar
thermodynamic stabilities. The barrier to create the ICT polymorph,
however, is lower than that to make the CTC polymorph, because the
ICT polymorph has a small critical nucleus, but the critical nucleus
for the CTC polymorph is larger than what we can simulate. Moreover,
simulated thermal annealing shows that the activation barrier for
converting the CTC polymorph to the ICT polymorph is relatively modest.
Overall, the simulations explain both the observed structures and
the thermodynamics of F4TCNQ-doped P3HT and offer guidelines
for targeting the production of a desired polymorph for different
applications.