First-Principles Simulations of the Initial Phase of Self-Aggregation of a Cyanine Dye: Structure and Optical Spectra

Using first-principles simulations,
we investigated the initial
steps of the self-aggregation of the dye pseudoisocyanine (PIC) in
water. First, we performed molecular dynamics (MD) simulations of
the self-aggregation process, in which pile-of-coins oligomers ranging
from dimers to stacks of about 20 molecules formed. The oligomer structures
were found to be very flexible, with the dimers entering a weakly
coupled state and then returning to a stable π–π
stacked conformation on a nanosecond time scale. The structural information
from the MD simulations was combined with quantum chemical calculations
to generate a time-dependent Frenkel exciton Hamiltonian for monomers,
dimers, and trimers, which included vibronic coupling. This Hamiltonian,
in turn, was used to calculate the absorption spectra for these systems.
The simulated dimer spectrum compared well to experiment, validating
the face-to-face stacked dimer arrangement found in our MD simulations.
Comparison of the simulated trimer spectrum to experiment suggested
that oligomers larger than the dimer cannot be abundant at the onset
of J-aggregation. Finally, the conformation of the PIC J-aggregate
was investigated by testing the stability of several possible conformations
in our MD simulations; none of the tested structures was found to
be stable.