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

Abstract

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.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

“…Initial attempts in this direction can be found in a number of publications. 41 , 179 , 180 All these results combined suggest that interatomic distances, on both Å and tens of nanometres scale, can reliably be extracted from MD simulations.…”

“…Their behaviour in solution and aggregates can be tuned using different substituents such that well-ordered nanostructures are formed as evidenced by cryo-TEM. 43 , 201 , 213 , 214 In principle the spontaneous assembly of such systems can be studied using MD simulation, as evidenced by Haverkort et al 41 An amphiphile pseudoisocyanine dye, amphi-PIC, was studied by MD simulations and two types of aggregates, single-walled tubes and ribbons were generated. However, it was found that the final arrangement of the self-assembled structure lacks long-range order.…”

“…A nice example of the difficulty that simulations at the all-atom level face to obtain equilibrated self-assembled structures is provided by the work of Haverkort et al 41 They performed extensive self-assembly simulations of amphi-pseudoisocyanine, a dye that forms highly ordered, single-walled cylindrical J-aggregates in experiment, see Fig. 3 .…”

Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra

“…Again, pioneering work was provided by Knoester and co-workers, who studied the spontaneous self-aggregation of an alkyl-substituted pseudoisocyanine (amphi-PIC) in aqueous solution by molecular dynamics simulations. 24 Cylindrical and ribbon-like conformations were suggested as possible candidates for the equilibrium structure, but due to the finite simulation times (200–700 ns) it could not be decided which of the two structures is more likely. In contrast, cryo-TEM images suggest 25 that the investigated amphi-PIC dye forms double-walled tubes and multilamellar spherical aggregates, at least at high dye concentrations.…”

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

“…In addition, the averaged MD structure was translated and rotated separately for each group To compare the performance of the polarizable CHARMM force eld with that of the nonpolarizable GROMOS force eld (which we used in our previous work 32,33 ) in reproducing PIC properties, we have also used the GROMOS force eld to simulate the crystal structure (the results are shown in Table 1). The GROMOS force eld performs considerably worse than CHARMM, resulting in signicantly larger RMSD values, especially for the PIC atoms, for which the RMSD value is 2.4 times bigger than the CHARMM result.…”