Molecular Dynamics Study of Self-Assembly of Aqueous Solutions of Poly[9,9-bis(4-Sulfonylbutoxyphenylphenyl) Fluorene-2,7-diyl-2,2’-Bithiophene] (PBS-PF2T) in the Presence of Pentaethylene Glycol Monododecyl Ether (C12E5)

Results are presented using molecular dynamics (MD) of the self-assembly of the conjugated polyelectrolyte poly[9,9-bis(4-sulfonylbutoxyphenylphenyl) fluorene-2,7-diyl-2,2’-bithiophene] (PBS-PF2T) with 680 mM pentaethylene glycol monododecyl ether (C12E5) in water. Simulations are used to examine the interaction between PBS-PF2T and C12E5 and suggest a break-up of PBS-PF2T aggregates in solution. These systems are dominated by the formation of cylindrical phases at temperatures between 0 °C and 20 °C and also between 45 °C and 90 °C. More diffuse phases are seen to occur between 20 °C and 45 °C and also above 90 °C. Simulations are related to previous computational and experimental studies on PBS-PF2T aggregation in the presence of tetraethylene glycol monododecyl ether (C12E4) in bulk and thin films.

. Simulation cell representation of (a) front view; and (b) side view of 680 mM C12E5 with two equivalents of PBS-PF2T at 45 °C after 10 ns, system 4. (PBS-PF2T is shown in van der Waals representations and solvent is omitted for clarity).  Figure S4. Simulation cell representation of (a) front view; (b) side view of simulation at 0 °C extended to 20 ns, system 1. Representation of (c) front view; (d) side view of simulation at 0 °C from starting structure B at 20 ns, system 1b. Representation of (e) front view; (f) side view of simulation at 0 °C from starting structure C at 20 ns, system 1c.
(e) (f) Figure S5. Simulation cell representation of (a) front view; (b) side view of simulation at 10 °C from starting structure B at 20 ns, system 2b. Figure S6. Simulation cell representation of (a) front view; (b) side view of simulation at 20 °C from starting structure B at 20 ns, system 3b.
. Simulation cell representation of (a) front view; (b) side view of simulation at 45 °C from starting structure B at 20 ns, system 4b. Representation of (c) front view; (d) side view of simulation at 45 °C from starting structure D at 20 ns, system 4d. Representation of (e) front view; (f) side view of simulation at 45 °C from original structure at 10 ns with black background showing the formation of three other loosely populated cylindrical arrangements, system 4. Figure S8. Cont.
(e) (f) Figure S8. Simulation cell representation of (a) front view; (b) side view of simulation at 45 °C from starting structure B at 20 ns, system 5b. Representation of (c) front view; (d) side view of simulation at 45 °C from starting structure C at 20 ns, system 5c. Representation of (e) front view; (f) side view of simulation at 45 °C from starting structure D at 20 ns, system 5d. Figure S9. Simulation cell representation of (a) front view; (b) side view of simulation at 90 °C from starting structure B at 20 ns, system 6b.         Random starting structures were generated by using -random seed option in genbox command. For the previous stuy where C12E4 was used as the surfactant [27], the number of C12E4 molecules required to fill 25% 680 mM of the cell of dimension 10 × 10 × 10 nm 3 was determined by calculating the weight of the cell containing the two equivalents of PBS-PF2T and the rest of the volume of the cell is filled with water (2 equivalents of PBS-PF2T and 29,744 H2O molecules had a total weight 540,104 g·mol −1 ) it could then be calculated that, in order for 25% 680 mM of this volume to contain non-ionic surfactant, 373 equivalents of C12E4 needed to be added (540,104 × 0.25 = 135,026 g·mol −1 → 135,026/362 g·mol −1 = 373 equivalents of C12E4). For the simulation of ten equivalents of PBS-PF2T, ten PBS-PF2T species were added to a simulation cell of 10 × 10 × 10 nm 3 with 60 Na + ions and 22,992 solvent molecules.
Simulated annealing was performed between 10 °C and 20 °C, the entire system was coupled to 293 K (20 °C) from system 3 and a trajectory was run at 293 K (20 °C) for 10 ns, between 10 and 15 ns the system was cooled to 283 K (10 °C) and the trajectory was run for a further 20 ns making a total simulation time of 35 ns. Table S5. Showing the calculated number of contacts below 0.6 nm in the first and final frames of the simulation demonstrating the closer proximity of the side chains with the solvent for systems 1-6. Contacts were calculated using the g_mindist command in gromacs.   In each case equilibration occurs rapidly and remains at a constant energy throughout the simulation and also persists close to the target temperature.
Micropaprticles applied into the central lumen. Scale bar is 1 cm.