Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations

We perform molecular dynamics (MD)
simulations of the self-assembly
process of pseudoisocyanine dye molecules with amphiphilic substituents
(amphi-PIC). The spontaneous aggregation of cyanine
molecules into large molecular J-aggregates with optical functionality
has drawn attention for many decades already, but the shape and molecular
structure of the aggregates remain issues of debate, as current imaging
techniques still lack molecular scale resolution. Our MD simulations
for amphi-PIC predict the existence of aggregates
with the shape of either a single-walled cylinder or a ribbon. We
characterize the internal structure of these aggregates using the
π–π stacking and the average orientation of the
long axis of the amphi-PIC molecule’s chromophore.
The molecular arrangement obtained exhibits much disorder, which may
explain the wide absorption band observed for aggregates of amphi-PIC. We show that changing the counterion of the positively
charged amphi-PIC dye can change the equilibrium
aggregate shape. In addition, we demonstrate that the cylindrical
aggregates attract each other and form bundles.