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

Abstract

Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.

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

“…In many cases, the simulated optical spectra present good agreement with the experimental measurements when disorder is taken into account. 43 , 207 Also note that the CD signal calculated by exciton methods typically covers only the supramolecular component of the signal and molecular chirality should be subtracted. However, many studies have demonstrated that the induced CD signal by assembly is generally significantly different or larger than the molecular component, such as for protein secondary structure determination 208 and achiral molecules forming helical assemblies.…”

“…In practice, this means that the initial configurations are under a lot of stress, leading either to numerical instabilities or causing distortion or even disintegration of the aggregate. Careful minimization and equilibration runs are therefore usually required, The work of Megow et al 43 on J-aggregates provides a nice example of this procedure. They use different wrapping and packing motifs to create aggregates of tetrachloro-tetraethyl-benzimidacarbocyanine (TTBC) dyes.…”

Dye Aggregates in Luminescent Solar Concentrators

“…The Stokes shift is also reasonably large compared to the width of the J‐band. Another promising aggregate is the cyanine derivative 5,5′,6,6′‐ tetrachloro‐1,1′,3,3′‐tetraethyl‐benzimidacarbocyanine (TTBC) …”

“…Another promising aggregate is the cyanine derivative 5,5 0 ,6,6 0 -tetrachloro-1,1 0 ,3,3 0 -tetraethyl-benzimidacarbocyanine (TTBC). [28] As mentioned above, in principle one has a large tunability of the properties of the JH-aggregate by choosing appropriate molecules and designing specific arrangements. In this way, nowadays one has the possibility to tailor the spectral properties in order to produce the JH-aggregates most suited for use in LSCs.…”

Exciton-Exciton Annihilation as a Mechanism for Uphill Transfer in a Molecular Excitonic System

“…According to cryo-transmission electron microscopy, TTBC-Cl forms single-walled tubes with a diameter of only 35 Å and lengths in the µm range [3]. Recently, a molecular structure was suggested, consistent with these dimensions and the absorption and LD spectra [5]. The structure is helical, formed by rings of six monomeric units with transition dipoles aligned 74° to the longitudinal aggregate axis, and an interring slip of 30°.…”